R-universe search: hta2.0

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

17.3 match 989 stars 20.56 score 29k scripts 4.3k dependents

topepo

C50:C5.0 Decision Trees and Rule-Based Models

C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).

Maintained by Max Kuhn. Last updated 2 years ago.

26.0 match 50 stars 11.99 score 1.3k scripts 13 dependents

stuart-lab

Signac:Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Maintained by Tim Stuart. Last updated 7 months ago.

atac bioinformatics single-cell zlib cpp

20.5 match 349 stars 12.19 score 3.7k scripts 1 dependents

biomodhub

biomod2:Ensemble Platform for Species Distribution Modeling

Functions for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. The package permits to run consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences) dataset and to combine them in ensemble models and ensemble projections. Some bench of other evaluation and visualisation tools are also available within the package.

Maintained by Maya Gueguen. Last updated 5 days ago.

16.9 match 95 stars 13.88 score 536 scripts 7 dependents

business-science

tidyquant:Tidy Quantitative Financial Analysis

Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.

Maintained by Matt Dancho. Last updated 1 months ago.

dplyr financial-analysis financial-data financial-statements multiple-stocks performance-analysis performanceanalytics quantmod stock stock-exchanges stock-indexes stock-lists stock-performance stock-prices stock-symbol tidyverse time-series timeseries xts

17.0 match 872 stars 13.34 score 5.2k scripts

utiligize

CNAIM:Common Network Asset Indices Methodology (CNAIM)

Implementation of the CNAIM standard in R. Contains a series of algorithms which determine the probability of failure, consequences of failure and monetary risk associated with electricity distribution companies' assets such as transformers and cables. Results are visualized in an easy-to-understand risk matrix.

Maintained by Mohsin Vindhani. Last updated 3 years ago.

34.4 match 5 stars 6.17 score 85 scripts

jbdorey

BeeBDC:Occurrence Data Cleaning

Flags and checks occurrence data that are in Darwin Core format. The package includes generic functions and data as well as some that are specific to bees. This package is meant to build upon and be complimentary to other excellent occurrence cleaning packages, including 'bdc' and 'CoordinateCleaner'. This package uses datasets from several sources and particularly from the Discover Life Website, created by Ascher and Pickering (2020). For further information, please see the original publication and package website. Publication - Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.

Maintained by James B. Dorey. Last updated 4 months ago.

28.4 match 3 stars 5.68 score 7 scripts

tvganesh

QCSimulator:5 Qubit Quantum Computing Simulator

This package simulates a 5 qubit Quantum Computer.

Maintained by Tinniam V Ganesh. Last updated 9 years ago.

33.8 match 5 stars 4.20 score 64 scripts

richarddmorey

BayesFactor:Computation of Bayes Factors for Common Designs

A suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.

Maintained by Richard D. Morey. Last updated 1 years ago.

cpp

9.6 match 133 stars 13.70 score 1.7k scripts 21 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

8.8 match 207 stars 12.89 score 768 scripts 51 dependents

bioc

PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

Maintained by Benjamin Haibe-Kains. Last updated 2 months ago.

geneexpression pharmacogenetics pharmacogenomics software classification datasets pharmacogenomic pharmacogx cpp

9.7 match 68 stars 11.39 score 442 scripts 3 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

8.1 match 845 stars 13.57 score 264 scripts 2 dependents

rdatatable

data.table:Extension of `data.frame`

Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

Maintained by Tyson Barrett. Last updated 4 hours ago.

4.7 match 3.7k stars 23.52 score 230k scripts 4.6k dependents

pcruniversum

chipPCR:Toolkit of Helper Functions to Pre-Process Amplification Data

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Maintained by Stefan Roediger. Last updated 4 years ago.

16.0 match 8 stars 6.84 score 97 scripts 1 dependents

svmiller

peacesciencer:Tools and Data for Quantitative Peace Science Research

These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.

Maintained by Steve Miller. Last updated 3 days ago.

eugene peace-science

19.8 match 29 stars 5.49 score 211 scripts

r-lib

backports:Reimplementations of Functions Introduced Since R-3.0.0

Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.

Maintained by Michel Lang. Last updated 7 months ago.

backports

8.2 match 66 stars 13.11 score 174 scripts 3.3k dependents

kwb-r

kwb.pilot:Importing, Aggregating and Visualising Data From KWB Pilot Plants

Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).

Maintained by Michael Rustler. Last updated 2 years ago.

data-aggregation data-import data-visualisation project-aquanes project-mbr40 project-suleman project-ultimate

24.7 match 1 stars 4.01 score 17 scripts

tidyverse

dbplyr:A 'dplyr' Back End for Databases

A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.

Maintained by Hadley Wickham. Last updated 3 months ago.

database

5.0 match 481 stars 19.72 score 5.2k scripts 736 dependents

r-forge

CHNOSZ:Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

Maintained by Jeffrey Dick. Last updated 8 days ago.

fortran

10.4 match 9.46 score 238 scripts 4 dependents

r-lib

scales:Scale Functions for Visualization

Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

ggplot2

4.9 match 419 stars 19.88 score 88k scripts 7.9k dependents

bioc

puma:Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Maintained by Xuejun Liu. Last updated 5 months ago.

microarray onechannel preprocessing differentialexpression clustering exonarray geneexpression mrnamicroarray chiponchip alternativesplicing differentialsplicing bayesian twochannel dataimport hta2.0

21.4 match 4.53 score 17 scripts

ropensci

getCRUCLdata:'CRU' 'CL' v. 2.0 Climatology Client

Provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a list of 'terra' 'rast' objects for use. 'CRU' 'CL' v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.

Maintained by Adam H. Sparks. Last updated 11 days ago.

anglia-cru climate-data cru-cl2 temperature rainfall elevation data-access wind relative-humidity solar-radiation diurnal-temperature frost cru peer-reviewed

14.2 match 18 stars 6.83 score 18 scripts

klausherrmann

multIntTestFunc:Provides Test Functions for Multivariate Integration

Provides implementations of functions that can be used to test multivariate integration routines. The package covers six different integration domains (unit hypercube, unit ball, unit sphere, standard simplex, non-negative real numbers and R^n). For each domain several functions with different properties (smooth, non-differentiable, ...) are available. The functions are available in all dimensions n >= 1. For each function the exact value of the integral is known and implemented to allow testing the accuracy of multivariate integration routines. Details on the available test functions can be found at on the development website.

Maintained by Klaus Herrmann. Last updated 6 months ago.

22.2 match 4.30 score 1 scripts

bjw34032

waveslim:Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing

Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.

Maintained by Brandon Whitcher. Last updated 10 months ago.

wavelets

12.0 match 3 stars 7.88 score 108 scripts 23 dependents

rstudio

tfprobability:Interface to 'TensorFlow Probability'

Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

10.8 match 54 stars 8.63 score 221 scripts 3 dependents

dchristop

inflection:Finds the Inflection Point of a Curve

Implementation of methods Extremum Surface Estimator (ESE) and Extremum Distance Estimator (EDE) to identify the inflection point of a curve . Christopoulos, DT (2014) <doi:10.48550/arXiv.1206.5478> . Christopoulos, DT (2016) <https://veltech.edu.in/wp-content/uploads/2016/04/Paper-04-2016.pdf> . Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> .

Maintained by Demetris T. Christopoulos. Last updated 3 years ago.

16.0 match 5.30 score 52 scripts 6 dependents

stevenmmortimer

salesforcer:An Implementation of 'Salesforce' APIs Using Tidy Principles

Functions connecting to the 'Salesforce' Platform APIs (REST, SOAP, Bulk 1.0, Bulk 2.0, Metadata, Reports and Dashboards) <https://trailhead.salesforce.com/content/learn/modules/api_basics/api_basics_overview>. "API" is an acronym for "application programming interface". Most all calls from these APIs are supported as they use CSV, XML or JSON data that can be parsed into R data structures. For more details please see the 'Salesforce' API documentation and this package's website <https://stevenmmortimer.github.io/salesforcer/> for more information, documentation, and examples.

Maintained by Steven M. Mortimer. Last updated 4 months ago.

api-wrappers r-language r-programming salesforce salesforce-apis

9.1 match 82 stars 9.27 score 191 scripts

stan-dev

loo:Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models

Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>. The approximation uses Pareto smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.

Maintained by Jonah Gabry. Last updated 3 days ago.

bayes bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics cross-validation information-criterion model-comparison stan

4.8 match 152 stars 17.30 score 2.6k scripts 297 dependents

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

5.0 match 520 stars 16.52 score 1.4k scripts 38 dependents

mrc-ide

EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

Maintained by Anne Cori. Last updated 7 months ago.

6.9 match 95 stars 12.00 score 1.0k scripts 7 dependents

r-lib

rlang:Functions for Base Types and Core R and 'Tidyverse' Features

A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

Maintained by Lionel Henry. Last updated 20 days ago.

4.0 match 517 stars 20.53 score 9.8k scripts 15k dependents

bluefoxr

COINr:Composite Indicator Construction and Analysis

A comprehensive high-level package, for composite indicator construction and analysis. It is a "development environment" for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation, data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single hierarchical list called a "coin". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons. It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results.

Maintained by William Becker. Last updated 2 months ago.

8.8 match 26 stars 9.07 score 73 scripts 1 dependents

functionaldata

fdapace:Functional Data Analysis and Empirical Dynamics

A versatile package that provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm. This core algorithm yields covariance and mean functions, eigenfunctions and principal component (scores), for both functional data and derivatives, for both dense (functional) and sparse (longitudinal) sampling designs. For sparse designs, it provides fitted continuous trajectories with confidence bands, even for subjects with very few longitudinal observations. PACE is a viable and flexible alternative to random effects modeling of longitudinal data. There is also a Matlab version (PACE) that contains some methods not available on fdapace and vice versa. Updates to fdapace were supported by grants from NIH Echo and NSF DMS-1712864 and DMS-2014626. Please cite our package if you use it (You may run the command citation("fdapace") to get the citation format and bibtex entry). References: Wang, J.L., Chiou, J., Müller, H.G. (2016) <doi:10.1146/annurev-statistics-041715-033624>; Chen, K., Zhang, X., Petersen, A., Müller, H.G. (2017) <doi:10.1007/s12561-015-9137-5>.

Maintained by Yidong Zhou. Last updated 9 months ago.

cpp

6.6 match 31 stars 11.46 score 474 scripts 25 dependents

r-lib

gitcreds:Query 'git' Credentials from 'R'

Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. This package is to be used by other packages that need to authenticate to 'GitHub' and/or other 'git' repositories.

Maintained by Gábor Csárdi. Last updated 7 months ago.

credentials credentials-helper git github

5.6 match 28 stars 13.28 score 372 scripts 405 dependents

rolkra

explore:Simplifies Exploratory Data Analysis

Interactive data exploration with one line of code, automated reporting or use an easy to remember set of tidy functions for low code exploratory data analysis.

Maintained by Roland Krasser. Last updated 3 months ago.

data-exploration data-visualisation decision-trees eda rmarkdown shiny tidy

6.5 match 228 stars 11.43 score 221 scripts 1 dependents

rstudio

pins:Pin, Discover, and Share Resources

Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'Posit Connect', 'AWS S3', and more.

Maintained by Julia Silge. Last updated 1 months ago.

azure gcloud rpins rsconnect s3 storage

5.3 match 321 stars 14.17 score 1.9k scripts 17 dependents

d-score

childdevdata:Child Development Data

Measuring child development starts by collecting responses to developmental milestones, such as "able to sit" or "says two words". There are many ways to combine such responses into summaries. The package bundles publicly available datasets with individual milestone data for children aged 0-5 years, with the aim of supporting the construction, evaluation, validation and interpretation of methodologies that aggregate milestone data into informative measures of child development.

Maintained by Stef van Buuren. Last updated 2 years ago.

child-development d-score dataset

23.4 match 3 stars 3.18 score 8 scripts

usepa

tcpl:ToxCast Data Analysis Pipeline

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Maintained by Jason Brown. Last updated 3 days ago.

ccte comptox ord

7.7 match 36 stars 9.41 score 90 scripts

cbielow

PTXQC:Quality Report Generation for MaxQuant and mzTab Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Maintained by Chris Bielow. Last updated 1 years ago.

drag-and-drop hacktoberfest heatmap match-between-runs maxquant metric mztab openms proteomics quality-control quality-metrics report

7.7 match 42 stars 9.35 score 105 scripts 1 dependents

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 7 days ago.

4.5 match 100 stars 15.36 score 1.4k scripts 36 dependents

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 30 days ago.

brain mri mrs mrshub spectroscopy fortran

8.1 match 25 stars 8.52 score 81 scripts

bioc

enrichViewNet:From functional enrichment results to biological networks

This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

Maintained by Astrid Deschênes. Last updated 5 months ago.

biologicalquestion software network networkenrichment go cystocape functional-enrichment

12.3 match 5 stars 5.54 score 6 scripts

wilkelab

cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'

Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.

Maintained by Claus O. Wilke. Last updated 2 months ago.

3.6 match 714 stars 18.83 score 75k scripts 1.4k dependents

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 19 days ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

6.8 match 126 stars 9.90 score 226 scripts 2 dependents

brodieg

vetr:Trust, but Verify

Declarative template-based framework for verifying that objects meet structural requirements, and auto-composing error messages when they do not.

Maintained by Brodie Gaslam. Last updated 9 months ago.

argument-checks input-validation

9.0 match 79 stars 7.50 score 67 scripts 1 dependents

alexkowa

EnvStats:Package for Environmental Statistics, Including US EPA Guidance

Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <doi:10.1007/978-1-4614-8456-1>).

Maintained by Alexander Kowarik. Last updated 17 days ago.

5.2 match 26 stars 12.80 score 2.4k scripts 46 dependents

stephens999

ashr:Methods for Adaptive Shrinkage, using Empirical Bayes

The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accommodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal).

Maintained by Peter Carbonetto. Last updated 10 months ago.

cpp

5.2 match 82 stars 12.10 score 780 scripts 15 dependents

hubverse-org

hubUtils:Core 'hubverse' Utilities

Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> for an overview of Collaborative Hubs.

Maintained by Anna Krystalli. Last updated 4 days ago.

hubverse

8.6 match 6 stars 7.22 score 49 scripts 7 dependents

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 4 days ago.

cdisc clinical-trials open-source

4.4 match 236 stars 13.89 score 486 scripts 4 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

3.9 match 146 stars 15.42 score 4.2k scripts 18 dependents

vinhdizzo

IRexamples:Collection of Practical Institutional Research Examples and Tutorials

Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.

Maintained by Vinh Nguyen. Last updated 2 years ago.

12.1 match 4 stars 5.00 score 4 scripts

amsantac

geospt:Geostatistical Analysis and Design of Optimal Spatial Sampling Networks

Estimation of the variogram through trimmed mean, radial basis functions (optimization, prediction and cross-validation), summary statistics from cross-validation, pocket plot, and design of optimal sampling networks through sequential and simultaneous points methods.

Maintained by Ali Santacruz. Last updated 6 days ago.

13.2 match 4 stars 4.56 score 30 scripts 1 dependents

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

5.1 match 5 stars 11.31 score 9.2k scripts 361 dependents

r-lib

vctrs:Vector Helpers

Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.

Maintained by Davis Vaughan. Last updated 5 months ago.

s3-vectors

3.0 match 290 stars 18.97 score 1.1k scripts 13k dependents

bioc

mirTarRnaSeq:mirTarRnaSeq

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.

Maintained by Mercedeh Movassagh. Last updated 5 months ago.

mirna regression software sequencing smallrna timecourse differentialexpression

14.2 match 4.00 score 9 scripts

timelyportfolio

sunburstR:Sunburst 'Htmlwidget'

Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.

Maintained by Kent Russell. Last updated 2 years ago.

chart d3 htmlwidgets interactive javascript visualization

5.6 match 210 stars 10.02 score 310 scripts 4 dependents

mbtyers

riverdist:River Network Distance Computation and Applications

Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.

Maintained by Matt Tyers. Last updated 4 months ago.

7.5 match 26 stars 7.50 score 96 scripts

ryo-n7

tvthemes:TV Show Themes and Color Palettes for 'ggplot2' Graphics

Contains various 'ggplot2' themes and color palettes based on TV shows such as 'Game of Thrones', 'Brooklyn Nine-Nine', 'Avatar: The Last Airbender', 'Spongebob Squarepants', and more.

Maintained by Ryo Nakagawara. Last updated 1 years ago.

color-scheme data-viz ggplot2 ggplot2-themes palette-colors tv-series tv-shows

7.6 match 140 stars 7.34 score 103 scripts

snoweye

phyclust:Phylogenetic Clustering (Phyloclustering)

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Maintained by Wei-Chen Chen. Last updated 2 years ago.

6.5 match 9 stars 8.45 score 126 scripts 8 dependents

klmr

box:Write Reusable, Composable and Modular R Code

A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.

Maintained by Konrad Rudolph. Last updated 13 days ago.

modules packages

4.4 match 888 stars 12.39 score 47 scripts 4 dependents

r-forge

copula:Multivariate Dependence with Copulas

Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

Maintained by Martin Maechler. Last updated 11 days ago.

4.6 match 11.83 score 1.2k scripts 86 dependents

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

3.6 match 113 stars 14.88 score 266 scripts 192 dependents

talgalili

heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.

Maintained by Tal Galili. Last updated 8 months ago.

d3-heatmap dendextend dendrogram ggplot2 heatmap plotly

3.6 match 386 stars 14.21 score 2.0k scripts 45 dependents

cran

autoRasch:Semi-Automated Rasch Analysis

Performs Rasch analysis (semi-)automatically, which has been shown to be comparable with the standard Rasch analysis (Feri Wijayanto et al. (2021) <doi:10.1111/bmsp.12218>, Feri Wijayanto et al. (2022) <doi:10.3758/s13428-022-01947-9>, Feri Wijayanto et al. (2022) <doi:10.1177/01466216221125178>).

Maintained by Feri Wijayanto. Last updated 2 years ago.

openblas cpp openmp

17.1 match 3.00 score

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

4.8 match 57 stars 10.66 score 944 scripts 15 dependents

business-science

timetk:A Tool Kit for Working with Time Series

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.

Maintained by Matt Dancho. Last updated 1 years ago.

coercion coercion-functions data-mining dplyr forecast forecasting forecasting-models machine-learning series-decomposition series-signature tibble tidy tidyquant tidyverse time time-series timeseries

3.6 match 625 stars 14.15 score 4.0k scripts 16 dependents

husson

FactoMineR:Multivariate Exploratory Data Analysis and Data Mining

Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).

Maintained by Francois Husson. Last updated 3 months ago.

3.3 match 47 stars 14.71 score 5.6k scripts 112 dependents

ajsmit

RmarineHeatWaves:Detect Marine Heat Waves and Marine Cold Spells

Given a time series of daily temperatures, the package provides tools to detect extreme thermal events, including marine heat waves, and to calculate the exceedances above or below specified threshold values. It outputs the properties of all detected events and exceedances.

Maintained by Albertus J. Smit. Last updated 6 years ago.

10.0 match 9 stars 4.88 score 17 scripts

mqbssppe

fabMix:Overfitting Bayesian Mixtures of Factor Analyzers with Parsimonious Covariance and Unknown Number of Components

Model-based clustering of multivariate continuous data using Bayesian mixtures of factor analyzers (Papastamoulis (2019) <DOI:10.1007/s11222-019-09891-z> (2018) <DOI:10.1016/j.csda.2018.03.007>). The number of clusters is estimated using overfitting mixture models (Rousseau and Mengersen (2011) <DOI:10.1111/j.1467-9868.2011.00781.x>): suitable prior assumptions ensure that asymptotically the extra components will have zero posterior weight, therefore, the inference is based on the ``alive'' components. A Gibbs sampler is implemented in order to (approximately) sample from the posterior distribution of the overfitting mixture. A prior parallel tempering scheme is also available, which allows to run multiple parallel chains with different prior distributions on the mixture weights. These chains run in parallel and can swap states using a Metropolis-Hastings move. Eight different parameterizations give rise to parsimonious representations of the covariance per cluster (following Mc Nicholas and Murphy (2008) <DOI:10.1007/s11222-008-9056-0>). The model parameterization and number of factors is selected according to the Bayesian Information Criterion. Identifiability issues related to label switching are dealt by post-processing the simulated output with the Equivalence Classes Representatives algorithm (Papastamoulis and Iliopoulos (2010) <DOI:10.1198/jcgs.2010.09008>, Papastamoulis (2016) <DOI:10.18637/jss.v069.c01>).

Maintained by Panagiotis Papastamoulis. Last updated 1 years ago.

openblas cpp openmp

23.4 match 2.09 score 41 scripts 1 dependents

eriqande

CKMRpop:Forward-in-Time Simulation and Tallying of Pairwise Relationships

Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.

Maintained by Eric C. Anderson. Last updated 1 years ago.

noaa-omics-software cpp

9.1 match 4 stars 5.38 score 24 scripts

edm44

hydraulics:Basic Pipe and Open Channel Hydraulics

Functions for basic hydraulic calculations related to water flow in circular pipes both flowing full (under pressure), and partially full (gravity flow), and trapezoidal open channels. For pressure flow this includes friction loss calculations by solving the Darcy-Weisbach equation for head loss, flow or diameter, plotting a Moody diagram, matching a pump characteristic curve to a system curve, and solving for flows in a pipe network using the Hardy-Cross method. The Darcy-Weisbach friction factor is calculated using the Colebrook (or Colebrook-White equation), the basis of the Moody diagram, the original citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity flow, the Manning equation is used, again solving for missing parameters. The derivation of and solutions using the Darcy-Weisbach equation and the Manning equation are outlined in many fluid mechanics texts such as Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and rapidly-varied flow functions are included. For the Manning equation solutions, this package uses modifications of original code from the 'iemisc' package by Irucka Embry.

Maintained by Ed Maurer. Last updated 4 months ago.

9.5 match 9 stars 5.13 score 8 scripts

sqyu

genscore:Generalized Score Matching Estimators

Implementation of the Generalized Score Matching estimator in Yu et al. (2019) <http://jmlr.org/papers/v20/18-278.html> for non-negative graphical models (truncated Gaussian, exponential square-root, gamma, a-b models) and univariate truncated Gaussian distributions. Also includes the original estimator for untruncated Gaussian graphical models from Lin et al. (2016) <doi:10.1214/16-EJS1126>, with the addition of a diagonal multiplier.

Maintained by Shiqing Yu. Last updated 5 years ago.

density-estimation graphical-models interaction-models score-matching undirected-graphs

11.5 match 1 stars 4.18 score 3 scripts 1 dependents

talgalili

dendextend:Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Maintained by Tal Galili. Last updated 2 months ago.

2.8 match 154 stars 17.02 score 6.0k scripts 164 dependents

amalan-constat

fitODBOD:Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD

Contains Probability Mass Functions, Cumulative Mass Functions, Negative Log Likelihood value, parameter estimation and modeling data using Binomial Mixture Distributions (BMD) (Manoj et al (2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>), also Journal article to use the package(<doi:10.21105/joss.01505>).

Maintained by Amalan Mahendran. Last updated 4 months ago.

binomial-outcome-data overdispersion

10.8 match 1 stars 4.44 score 139 scripts

tomasfryda

h2o:R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Maintained by Tomas Fryda. Last updated 1 years ago.

5.8 match 3 stars 8.20 score 7.8k scripts 11 dependents

sherrillmix

taxonomizr:Functions to Work with NCBI Accessions and Taxonomy

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Maintained by Scott Sherrill-Mix. Last updated 4 days ago.

5.3 match 72 stars 8.85 score 255 scripts 2 dependents

ropensci

rix:Reproducible Data Science Environments with 'Nix'

Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.

Maintained by Bruno Rodrigues. Last updated 5 days ago.

nix peer-reviewed reproducibility reproducible-research

4.5 match 235 stars 10.54 score 67 scripts

pbs-software

PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data

Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.

Maintained by Rowan Haigh. Last updated 4 months ago.

6.9 match 2 stars 6.76 score 120 scripts 4 dependents

markedmondson1234

googleAuthR:Authenticate and Create Google APIs

Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.

Maintained by Erik Grönroos. Last updated 10 months ago.

api authentication google googleauthr oauth2-flow shiny

3.6 match 178 stars 12.84 score 804 scripts 13 dependents

frenchrh

klovan:Geostatistics Methods and Klovan Data

A comprehensive set of geostatistical, visual, and analytical methods, in conjunction with the expanded version of the acclaimed J.E. Klovan's mining dataset, are included in 'klovan'. This makes the package an excellent learning resource for Principal Component Analysis (PCA), Factor Analysis (FA), kriging, and other geostatistical techniques. Originally published in the 1976 book 'Geological Factor Analysis', the included mining dataset was assembled by Professor J. E. Klovan of the University of Calgary. Being one of the first applications of FA in the geosciences, this dataset has significant historical importance. As a well-regarded and published dataset, it is an excellent resource for demonstrating the capabilities of PCA, FA, kriging, and other geostatistical techniques in geosciences. For those interested in these methods, the 'klovan' datasets provide a valuable and illustrative resource. Note that some methods require the 'RGeostats' package. Please refer to the README or Additional_repositories for installation instructions. This material is based upon research in the Materials Data Science for Stockpile Stewardship Center of Excellence (MDS3-COE), and supported by the Department of Energy's National Nuclear Security Administration under Award Number DE-NA0004104.

Maintained by Roger H French. Last updated 1 years ago.

18.5 match 2.48 score

r-forge

DPQ:Density, Probability, Quantile ('DPQ') Computations

Computations for approximations and alternatives for the 'DPQ' (Density (pdf), Probability (cdf) and Quantile) functions for probability distributions in R. Primary focus is on (central and non-central) beta, gamma and related distributions such as the chi-squared, F, and t. -- For several distribution functions, provide functions implementing formulas from Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207> and Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous distributions respectively. This is for the use of researchers in these numerical approximation implementations, notably for my own use in order to improve standard R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.

Maintained by Martin Maechler. Last updated 1 months ago.

fortran

7.9 match 5.75 score 43 scripts 1 dependents

torewentzel-larsen

crossrun:Joint Distribution of Number of Crossings and Longest Run

Joint distribution of number of crossings and the longest run in a series of independent Bernoulli trials. The computations uses an iterative procedure where computations are based on results from shorter series. The procedure conditions on the start value and partitions by further conditioning on the position of the first crossing (or none).

Maintained by Tore Wentzel-Larsen. Last updated 3 years ago.

10.2 match 4.45 score 14 scripts

friendly

matlib:Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics

A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. Many of these functions are designed for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D and for rendering matrix expressions and equations in LaTeX.

Maintained by Michael Friendly. Last updated 2 days ago.

diagrams linear-equations matrix matrix-functions matrix-visualizer vector vignette

3.5 match 65 stars 12.89 score 900 scripts 11 dependents

bluegreen-labs

hwsdr:Interface to the 'HWSD' Web Services

Programmatic interface to the Harmonized World Soil Database 'HWSD' web services (<https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1247>). Allows for easy downloads of 'HWSD' soil data directly to your R workspace or your computer. Routines for both single pixel data downloads and gridded data are provided.

Maintained by Koen Hufkens. Last updated 10 months ago.

api-client modelling soil spatial-analyses spatial-data

8.7 match 16 stars 5.20 score 8 scripts

bioc

gCrisprTools:Suite of Functions for Pooled Crispr Screen QC and Analysis

Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

Maintained by Russell Bainer. Last updated 5 months ago.

immunooncology crispr pooledscreens experimentaldesign biomedicalinformatics cellbiology functionalgenomics pharmacogenomics pharmacogenetics systemsbiology differentialexpression genesetenrichment genetics multiplecomparison normalization preprocessing qualitycontrol rnaseq regression software visualization

9.2 match 4.78 score 8 scripts

tidyverse

tidyr:Tidy Messy Data

Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).

Maintained by Hadley Wickham. Last updated 13 days ago.

tidy-data cpp

1.9 match 1.4k stars 22.88 score 168k scripts 5.5k dependents

jayanilakshika

cardinalR:Collection of Data Structures

A collection of simple simulation datasets designed for generating Nonlinear Dimension Reduction representations techniques such as t-distributed Stochastic Neighbor Embedding, and Uniform Manifold Approximation and Projection. These datasets serve as a valuable resource for understanding the reliability of Nonlinear Dimension Reduction representations in various contexts.

Maintained by Jayani P.G. Lakshika. Last updated 12 days ago.

9.6 match 4.54 score

project-gen3sis

gen3sis:General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Maintained by Oskar Hagen. Last updated 1 years ago.

biodiversity ecology evolution mechanistic model modeling simulation cpp

5.7 match 29 stars 7.56 score 69 scripts

bioc

satuRn:Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.

Maintained by Jeroen Gilis. Last updated 5 months ago.

regression experimentaldesign differentialexpression geneexpression rnaseq sequencing software singlecell transcriptomics multiplecomparison visualization

6.1 match 21 stars 6.97 score 74 scripts 1 dependents

beirnaert

speaq:Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.

Maintained by Charlie Beirnaert. Last updated 3 years ago.

6.0 match 9 stars 7.02 score 26 scripts 3 dependents

hughjonesd

santoku:A Versatile Cutting Tool

A tool for cutting data into intervals. Allows singleton intervals. Always includes the whole range of data by default. Flexible labelling. Convenience functions for cutting by quantiles etc. Handles dates, times, units and other vectors.

Maintained by David Hugh-Jones. Last updated 10 months ago.

cpp

5.3 match 138 stars 8.00 score 108 scripts 2 dependents

ropenspain

climaemet:Climate AEMET Tools

Tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).

Maintained by Diego Hernangómez. Last updated 1 months ago.

aemet climate data forecast-api ropenspain science spain weather-api

5.0 match 43 stars 8.32 score 59 scripts

distancedevelopment

mrds:Mark-Recapture Distance Sampling

Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.

Maintained by Laura Marshall. Last updated 2 months ago.

5.2 match 4 stars 8.05 score 78 scripts 7 dependents

mcguinlu

robvis:Visualize the Results of Risk-of-Bias (ROB) Assessments

Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review. It allows users to create weighted bar-plots of the distribution of risk-of-bias judgments within each bias domain, in addition to traffic-light plots of the specific domain-level judgments for each study. The resulting figures are of publication quality and are formatted according the risk-of-bias assessment tool use to perform the assessments. Currently, the supported tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019) <doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of interventions; Sterne (2016) <doi:10.1136/bmj.i4919>), and Quality & Applicability of Diagnostic Accuracy Studies V2 (Whiting et al (2011) <doi:10.7326/0003-4819-155-8-201110180-00009>), and QUIPS (Hayden et al (2013) <doi:10.7326/0003-4819-158-4-201302190-00009>.

Maintained by Luke McGuinness. Last updated 2 years ago.

evidence-synthesis risk-of-bias systematic-reviews visualisation

5.2 match 59 stars 7.99 score 67 scripts

adwolfer

santaR:Short Asynchronous Time-Series Analysis

A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.

Maintained by Arnaud Wolfer. Last updated 1 years ago.

pcamethods (>= 1.92.0)

6.3 match 11 stars 6.44 score 63 scripts

inlabru-org

inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.

Maintained by Finn Lindgren. Last updated 4 days ago.

3.2 match 96 stars 12.62 score 832 scripts 6 dependents

adw96

breakaway:Species Richness Estimation and Modeling

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.

Maintained by Amy D Willis. Last updated 1 years ago.

4.9 match 68 stars 8.18 score 211 scripts

bioc

flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Maintained by Greg Finak. Last updated 10 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

5.1 match 7.89 score 576 scripts 10 dependents

dynverse

dynutils:Common Functionality for the 'dynverse' Packages

Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

cpp

5.8 match 3 stars 6.89 score 109 scripts 8 dependents

bioc

affy:Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Maintained by Robert D. Shear. Last updated 2 months ago.

microarray onechannel preprocessing

3.6 match 11.12 score 2.5k scripts 98 dependents

prajual

bqror:Bayesian Quantile Regression for Ordinal Models

Package provides functions for estimating Bayesian quantile regression with ordinal outcomes, computing the covariate effects, model comparison measures, and inefficiency factor. The generic ordinal model with 3 or more outcomes (labeled OR1 model) is estimated by a combination of Gibbs sampling and Metropolis-Hastings algorithm. Whereas an ordinal model with exactly 3 outcomes (labeled OR2 model) is estimated using Gibbs sampling only. For each model framework, there is a specific function for estimation. The summary output produces estimates for regression quantiles and two measures of model comparison — log of marginal likelihood and Deviance Information Criterion (DIC). The package also has specific functions for computing the covariate effects and other functions that aids either the estimation or inference in quantile ordinal models. Rahman, M. A. (2016).“Bayesian Quantile Regression for Ordinal Models.” Bayesian Analysis, II(I): 1-24 <doi: 10.1214/15-BA939>. Yu, K., and Moyeed, R. A. (2001). “Bayesian Quantile Regression.” Statistics and Probability Letters, 54(4): 437–447 <doi: 10.1016/S0167-7152(01)00124-9>. Koenker, R., and Bassett, G. (1978).“Regression Quantiles.” Econometrica, 46(1): 33-50 <doi: 10.2307/1913643>. Chib, S. (1995). “Marginal likelihood from the Gibbs output.” Journal of the American Statistical Association, 90(432):1313–1321, 1995. <doi: 10.1080/01621459.1995.10476635>. Chib, S., and Jeliazkov, I. (2001). “Marginal likelihood from the Metropolis-Hastings output.” Journal of the American Statistical Association, 96(453):270–281, 2001. <doi: 10.1198/016214501750332848>.

Maintained by Prajual Maheshwari. Last updated 3 years ago.

19.8 match 2.01 score 4 scripts

rjpeng98

ETASbootstrap:Bootstrap Confidence Interval Estimation for 'ETAS' Model Parameters

The 2-D spatial and temporal Epidemic Type Aftershock Sequence ('ETAS') Model is widely used to 'decluster' earthquake data catalogs. Usually, the calculation of standard errors of the 'ETAS' model parameter estimates is based on the Hessian matrix derived from the log-likelihood function of the fitted model. However, when an 'ETAS' model is fitted to a local data set over a time period that is limited or short, the standard errors based on the Hessian matrix may be inaccurate. It follows that the asymptotic confidence intervals for parameters may not always be reliable. As an alternative, this package allows for the construction of bootstrap confidence intervals based on empirical quantiles for the parameters of the 2-D spatial and temporal 'ETAS' model. This version improves on Version 0.1.0 of the package by enabling the study space window (renamed 'study region') to be polygonal rather than merely rectangular. A Japan earthquake data catalog is used in a second example to illustrate this new feature.

Maintained by Renjie Peng. Last updated 8 months ago.

12.0 match 2 stars 3.30 score 2 scripts

bioc

GenVisR:Genomic Visualizations in R

Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Maintained by Zachary Skidmore. Last updated 5 months ago.

infrastructure datarepresentation classification dnaseq

4.0 match 215 stars 9.87 score 76 scripts

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 2 months ago.

3.5 match 49 stars 11.25 score 332 scripts 2 dependents

iembry

ie2miscdata:Irucka Embry's Miscellaneous USGS Data Collection

A collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.

Maintained by Irucka Embry. Last updated 2 years ago.

9.8 match 4.00 score

cynkra

dm:Relational Data Models

Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.

Maintained by Kirill Müller. Last updated 2 months ago.

data-model data-warehousing datawarehousing dbi dbplyr relational-databases

2.6 match 511 stars 14.81 score 410 scripts 8 dependents

hughparsonage

hutils:Miscellaneous R Functions and Aliases

Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.

Maintained by Hugh Parsonage. Last updated 2 years ago.

5.0 match 12 stars 7.76 score 219 scripts 8 dependents

kwb-r

aquanes.report:Automated Reporting Tool for Water Suppliers

Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).

Maintained by Michael Rustler. Last updated 6 years ago.

automated-reporting data-aggregation data-export data-import data-visualisation pilot-plant project-aquanes shiny-app

9.5 match 4.01 score 23 scripts

ishidamgm

TreeRingShape:Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing and Interpolating Model

Record all tree-ring Shapefile of tree disk with GIS soft ('Qgis'<https://www.qgis.org/en/site/>) and interpolating model from high resolution tree disk image.

Maintained by Megumi ISHIDA. Last updated 4 months ago.

8.5 match 4.48 score

pbourkey

polymapR:Linkage Analysis in Outcrossing Polyploids

Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Maintained by Peter Bourke. Last updated 10 months ago.

9.4 match 1 stars 4.03 score 54 scripts

pendy05

vDiveR:Visualization of Viral Protein Sequence Diversity Dynamics

To ease the visualization of outputs from Diversity Motif Analyser ('DiMA'; <https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity motifs (index and its variants – major, minor and unique) for elucidation of the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/> for more information.

Maintained by Pendy Tok. Last updated 1 months ago.

conservation-level diversity entropy sequences viral visualization

10.0 match 3.78 score 4 scripts

benrwoodard

adobeanalyticsr:R Client for 'Adobe Analytics' API 2.0

Connect to the 'Adobe Analytics' API v2.0 <https://github.com/AdobeDocs/analytics-2.0-apis> which powers 'Analysis Workspace'. The package was developed with the analyst in mind, and it will continue to be developed with the guiding principles of iterative, repeatable, timely analysis.

Maintained by Ben Woodard. Last updated 2 months ago.

5.3 match 18 stars 7.02 score 39 scripts

icarda-git

QBMS:Query the Breeding Management System(s)

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.

Maintained by Khaled Al-Shamaa. Last updated 6 months ago.

4.7 match 8 stars 7.85 score 33 scripts 1 dependents

bioc

ggbio:Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

3.0 match 111 stars 12.26 score 734 scripts 17 dependents

r-lib

webfakes:Fake Web Apps for HTTP Testing

Create a web app that makes it easier to test web clients without using the internet. It includes a web app framework with path matching, parameters and templates. Can parse various 'HTTP' request bodies. Can send 'JSON' data or files from the disk. Includes a web app that implements the 'httpbin.org' web service.

Maintained by Gábor Csárdi. Last updated 2 months ago.

5.0 match 63 stars 7.37 score 15 scripts 1 dependents

alexpate30

calibmsm:Calibration Plots for the Transition Probabilities from Multistate Models

Assess the calibration of an existing (i.e. previously developed) multistate model through calibration plots. Calibration is assessed using one of three methods. 1) Calibration methods for binary logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 2) Calibration methods for multinomial logistic regression models applied at a fixed time point in conjunction with inverse probability of censoring weights. 3) Pseudo-values estimated using the Aalen-Johansen estimator of observed risk. All methods are applied in conjunction with landmarking when required. These calibration plots evaluate the calibration (in a validation cohort of interest) of the transition probabilities estimated from an existing multistate model. While package development has focused on multistate models, calibration plots can be produced for any model which utilises information post baseline to update predictions (e.g. dynamic models); competing risks models; or standard single outcome survival models, where predictions can be made at any landmark time. Please see Pate et al. (2024) <doi:10.1002/sim.10094> and Pate et al. (2024) <https://alexpate30.github.io/calibmsm/articles/Overview.html>.

Maintained by Alexander Pate. Last updated 19 days ago.

6.7 match 2 stars 5.38 score 10 scripts

zachmayer

caretEnsemble:Ensembles of Caret Models

Functions for creating ensembles of caret models: caretList() and caretStack(). caretList() is a convenience function for fitting multiple caret::train() models to the same dataset. caretStack() will make linear or non-linear combinations of these models, using a caret::train() model as a meta-model.

Maintained by Zachary A. Deane-Mayer. Last updated 3 months ago.

3.0 match 226 stars 11.92 score 780 scripts 1 dependents

kbroman

broman:Karl Broman's R Code

Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.

Maintained by Karl W Broman. Last updated 10 months ago.

4.0 match 183 stars 8.80 score 648 scripts 1 dependents

r-forge

stops:Structure Optimized Proximity Scaling

Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of dissimilarities and configuration distances, elastic scaling powers of dissimilarities and configuration distances, Sammon mapping powers of dissimilarities and configuration distances, power stress MDS (POST-MDS), approximate power stress, Box-Cox MDS, local MDS, Isomap, curvilinear component analysis (CLCA), curvilinear distance analysis (CLDA) and sparsified (power) multidimensional scaling and (power) multidimensional distance analysis (experimental models from smacofx influenced by CLCA). All of these models can also be fit by optimizing over hyperparameters based on goodness-of-fit fit only (i.e., no structure considerations). The package further contains functions for optimization, specifically the adaptive Luus-Jaakola algorithm and a wrapper for Bayesian optimization with treed Gaussian process with jumps to linear models, and functions for various c-structuredness indices.

Maintained by Thomas Rusch. Last updated 2 months ago.

openjdk

7.9 match 1 stars 4.48 score 23 scripts

teos-10

gsw:Gibbs Sea Water Functions

Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C library, version 3.06-16-0 (commit '657216dd4f5ea079b5f0e021a4163e2d26893371', dated 2022-10-11, available at <https://github.com/TEOS-10/GSW-C>, which stems from 'Matlab' and other code written by members of Working Group 127 of 'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research / International Association for the Physical Sciences of the Oceans).

Maintained by Dan Kelley. Last updated 8 days ago.

gibbs oceanography seawater teos-10

4.1 match 8 stars 8.53 score 286 scripts 19 dependents

bnaras

cubature:Adaptive Multivariate Integration over Hypercubes

R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.

Maintained by Balasubramanian Narasimhan. Last updated 8 months ago.

fortran cpp

3.1 match 12 stars 11.08 score 488 scripts 162 dependents

r-forge

GNE:Computation of Generalized Nash Equilibria

Compute standard and generalized Nash Equilibria of non-cooperative games. Optimization methods available are nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.

Maintained by Christophe Dutang. Last updated 2 months ago.

6.1 match 1 stars 5.65 score 14 scripts

pepijn-devries

adfExplorer:Access and Manipulate Amiga Disk Files

Amiga Disk Files (ADF) are virtual representations of 3.5 inch floppy disks for the Commodore Amiga. Most disk drives from other systems (including modern drives) are not able to read these disks. The 'adfExplorer' package enables you to establish R connections to files on such virtual DOS-formatted disks, which can be use to read from and write to those files.

Maintained by Pepijn de Vries. Last updated 2 months ago.

cpp

5.7 match 3 stars 5.94 score 36 scripts

bioc

BiocStyle:Standard styles for vignettes and other Bioconductor documents

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

software bioconductor-package core-package

3.0 match 12 stars 11.33 score 1.2k scripts 47 dependents

bioc

ChIPpeakAnno:Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Maintained by Jianhong Ou. Last updated 2 months ago.

annotation chipseq chipchip

3.8 match 8.75 score 584 scripts 6 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 9 hours ago.

fortran cpp

2.0 match 87 stars 16.70 score 7.7k scripts 99 dependents

usaid-mozambique

sonata:Interagir com MozART 2.0

Provides a set of utilities and functions for connecting, querying, and analyzing data from the Mozambique MozART 2.0 database.

Maintained by Joe Lara. Last updated 2 days ago.

8.1 match 4.08 score

r-barnes

dggridR:Discrete Global Grids

Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.

Maintained by Sebastian Krantz. Last updated 6 months ago.

discrete-global-grids geospatial spatial-analysis cpp

3.5 match 168 stars 9.37 score 388 scripts 1 dependents

japal

MALDIrppa:MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis

Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data (Palarea-Albaladejo et al. (2018) <doi:10.1093/bioinformatics/btx628>).

Maintained by Javier Palarea-Albaladejo. Last updated 1 years ago.

mass-spectrometry pre-processing

5.4 match 2 stars 6.06 score 32 scripts 1 dependents

hojsgaard

gRbase:A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.

Maintained by Søren Højsgaard. Last updated 4 months ago.

openblas cpp

3.5 match 3 stars 9.24 score 241 scripts 20 dependents

delosh653

mwshiny:'Shiny' for Multiple Windows

A simple function, mwsApp(), that runs a 'shiny' app spanning multiple, connected windows. This uses all standard 'shiny' conventions, and depends only on the 'shiny' package.

Maintained by Hannah De los Santos. Last updated 5 years ago.

5.5 match 25 stars 5.83 score 27 scripts

canmod

macpan2:Fast and Flexible Compartmental Modelling

Fast and flexible compartmental modelling with Template Model Builder.

Maintained by Steve Walker. Last updated 2 days ago.

compartmental-models epidemiology forecasting mixed-effects model-fitting optimization simulation simulation-modeling cpp

3.6 match 4 stars 8.89 score 246 scripts 1 dependents

matthieu-bruneaux

isotracer:Isotopic Tracer Analysis Using MCMC

Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.

Maintained by Matthieu Bruneaux. Last updated 4 months ago.

cpp

5.3 match 5.92 score 60 scripts

azure

AzureStor:Storage Management in 'Azure'

Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.

Maintained by Hong Ooi. Last updated 2 years ago.

azure-data-lake azure-sdk-r azure-storage azure-storage-blob azure-storage-file

2.9 match 64 stars 10.72 score 298 scripts 4 dependents

bioc

TFutils:TFutils

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

Maintained by Vincent Carey. Last updated 4 months ago.

transcriptomics

6.5 match 4.80 score 21 scripts

rinterface

shinydashboardPlus:Add More 'AdminLTE2' Components to 'shinydashboard'

Extend 'shinydashboard' with 'AdminLTE2' components. 'AdminLTE2' is a free 'Bootstrap 3' dashboard template available at <https://adminlte.io>. Customize boxes, add timelines and a lot more.

Maintained by David Granjon. Last updated 8 months ago.

dashboard hacktoberfest2022 shiny shiny-apps shinydashboard

2.3 match 459 stars 13.79 score 1.1k scripts 28 dependents

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

1.6 match 1.4k stars 19.15 score 35k scripts 231 dependents

zhenkewu

baker:"Nested Partially Latent Class Models"

Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>; Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>; Wu and Chen (2021) <doi:10.1002/sim.8804>) for inference of population disease etiology and individual diagnosis. In the motivating Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities of interest sum to one hundred percent, the PERCH scientists frequently refer to them as population etiology pie and individual etiology pie, hence the name of the package.

Maintained by Zhenke Wu. Last updated 11 months ago.

bayesian case-control latent-class-analysis jags cpp

5.2 match 8 stars 6.00 score 21 scripts

guillaumepressiat

pmeasyr:Donnees PMSI avec R

Import de donnees PMSI. Gestion des archives. Formats depuis 2011. Connexion et interface avec une db. requetr. Valorisation des rsa, des rapss.

Maintained by Guillaume Pressiat. Last updated 13 days ago.

had mco pmsi psy ssr

4.6 match 20 stars 6.76 score 53 scripts

pmartr

pmartR:Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Maintained by Lisa Bramer. Last updated 3 days ago.

data-summarization lipids mass-spectrometry metabolites metabolomics-data peptides proteins rna-seq-analysis openblas cpp

4.0 match 40 stars 7.69 score 144 scripts

pharmar

riskmetric:Risk Metrics to Evaluating R Packages

Facilities for assessing R packages against a number of metrics to help quantify their robustness.

Maintained by Eli Miller. Last updated 9 days ago.

3.4 match 167 stars 8.89 score 43 scripts

bioinformatics-ptp

detectRUNS:Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) <doi:10.1086/519795>) and consecutive runs (Marras et al (2015) <doi:10.1111/age.12259>).

Maintained by Filippo Biscarini. Last updated 3 years ago.

cpp

4.7 match 9 stars 6.50 score 35 scripts

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

2.8 match 81 stars 10.94 score 792 scripts

ropensci

rdhs:API Client and Dataset Management for the Demographic and Health Survey (DHS) Data

Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.

Maintained by OJ Watson. Last updated 17 days ago.

dataset dhs dhs-api extract peer-reviewed survey-data

3.0 match 35 stars 10.07 score 286 scripts 3 dependents

cardiomoon

ggiraphExtra:Make Interactive 'ggplot2'. Extension to 'ggplot2' and 'ggiraph'

Collection of functions to enhance 'ggplot2' and 'ggiraph'. Provides functions for exploratory plots. All plot can be a 'static' plot or an 'interactive' plot using 'ggiraph'.

Maintained by Keon-Woong Moon. Last updated 4 years ago.

3.4 match 48 stars 8.93 score 402 scripts 3 dependents

lindsayevanslee

whomds:Calculate Results from WHO Model Disability Survey Data

The Model Disability Survey (MDS) <https://www.who.int/activities/collection-of-data-on-disability> is a World Health Organization (WHO) general population survey instrument to assess the distribution of disability within a country or region, grounded in the International Classification of Functioning, Disability and Health <https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health>. This package provides fit-for-purpose functions for calculating and presenting the results from this survey, as used by the WHO. The package primarily provides functions for implementing Rasch Analysis (see Andrich (2011) <doi:10.1586/erp.11.59>) to calculate a metric scale for disability.

Maintained by Lindsay Lee. Last updated 2 years ago.

5.4 match 4 stars 5.56 score 15 scripts

resplab

cumulcalib:Cumulative Calibration Assessment for Prediction Models

Tools for visualization of, and inference on, the calibration of prediction models on the cumulative domain. This provides a method for evaluating calibration of risk prediction models without having to group the data or use tuning parameters (e.g., loess bandwidth). This package implements the methodology described in Sadatsafavi and Patkau (2024) <doi:10.1002/sim.10138>. The core of the package is cumulcalib(), which takes in vectors of binary responses and predicted risks. The plot() and summary() methods are implemented for the results returned by cumulcalib().

Maintained by Mohsen Sadatsafavi. Last updated 9 months ago.

6.5 match 2 stars 4.60 score 8 scripts

helske

Rlibeemd:Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN)

An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>, a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD). Due to the possible portability issues CRAN version no longer supports OpenMP, you can install OpenMP-supported version from GitHub: <https://github.com/helske/Rlibeemd/>.

Maintained by Jouni Helske. Last updated 2 years ago.

c decomposition eemd emd time-series gsl cpp openmp

4.9 match 39 stars 6.14 score 17 scripts 14 dependents

ausgis

geocomplexity:Mitigating Spatial Bias Through Geographical Complexity

The geographical complexity of individual variables can be characterized by the differences in local attribute variables, while the common geographical complexity of multiple variables can be represented by fluctuations in the similarity of vectors composed of multiple variables. In spatial regression tasks, the goodness of fit can be improved by incorporating a geographical complexity representation vector during modeling, using a geographical complexity-weighted spatial weight matrix, or employing local geographical complexity kernel density. Similarly, in spatial sampling tasks, samples can be selected more effectively by using a method that weights based on geographical complexity. By optimizing performance in spatial regression and spatial sampling tasks, the spatial bias of the model can be effectively reduced.

Maintained by Wenbo Lv. Last updated 4 months ago.

geographical-complexity geospatial-analysis spatial-regression spatial-relations spatial-sampling spatial-statistics openblas cpp openmp

4.5 match 19 stars 6.53 score 12 scripts

bcgov

bcdata:Search and Retrieve Data from the BC Data Catalogue

Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.

Maintained by Andy Teucher. Last updated 1 months ago.

bcdc citz data-science env

2.9 match 83 stars 10.29 score 186 scripts 4 dependents

cran

VFP:Variance Function Program

Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', www.aacb.asn.au/AACB/Resources/Variance-Function-Program). Here, the idea is to fit multiple variance functions to a data set and consequently assess which function reflects the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship is of great importance when individual test-results are used for defining follow-up treatment of patients.

Maintained by Andre Schuetzenmeister. Last updated 2 months ago.

9.8 match 3.01 score 17 scripts

ybrugnara

dataresqc:C3S Quality Control Tools for Historical Climate Data

Quality control and formatting tools developed for the Copernicus Data Rescue Service. The package includes functions to handle the Station Exchange Format (SEF), various statistical tests for climate data at daily and sub-daily resolution, as well as functions to plot the data. For more information and documentation see <https://datarescue.climate.copernicus.eu/st_data-quality-control>.

Maintained by Yuri Brugnara. Last updated 2 years ago.

10.8 match 2.70 score 7 scripts

rinterface

bs4Dash:A 'Bootstrap 4' Version of 'shinydashboard'

Make 'Bootstrap 4' Shiny dashboards. Use the full power of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4' <https://github.com/ColorlibHQ/AdminLTE>.

Maintained by David Granjon. Last updated 6 months ago.

bootstrap4 dashboard-templates hacktoberfest2022 shiny shiny-apps shinydashboard

2.3 match 442 stars 12.87 score 1.2k scripts 15 dependents

bioc

CINdex:Chromosome Instability Index

The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.

Maintained by Yuriy Gusev. Last updated 5 months ago.

software copynumbervariation genomicvariation acgh microarray genetics sequencing

7.1 match 4.08 score 2 scripts

ropensci

readODS:Read and Write ODS Files

Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.

Maintained by Chung-hong Chan. Last updated 2 months ago.

cpp

2.3 match 55 stars 12.74 score 808 scripts 26 dependents

tidymodels

parsnip:A Common API to Modeling and Analysis Functions

A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', 'H2O', etc).

Maintained by Max Kuhn. Last updated 4 days ago.

1.8 match 612 stars 16.37 score 3.4k scripts 69 dependents

crlsierra

SoilR:Models of Soil Organic Matter Decomposition

Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) <doi:10.5194/gmd-5-1045-2012> and Sierra and others (2014) <doi:10.5194/gmd-7-1919-2014>.

Maintained by Carlos A. Sierra. Last updated 1 years ago.

9.9 match 5 stars 2.88 score 153 scripts

stocnet

goldfish:Statistical Network Models for Dynamic Network Data

Tools for fitting statistical network models to dynamic network data. Can be used for fitting both dynamic network actor models ('DyNAMs') and relational event models ('REMs'). Stadtfeld, Hollway, and Block (2017a) <doi:10.1177/0081175017709295>, Stadtfeld, Hollway, and Block (2017b) <doi:10.1177/0081175017733457>, Stadtfeld and Block (2017) <doi:10.15195/v4.a14>, Hoffman et al. (2020) <doi:10.1017/nws.2020.3>.

Maintained by Alvaro Uzaheta. Last updated 7 months ago.

dynam network-modelling rem statistical-network-analysis openblas cpp openmp

3.6 match 61 stars 7.91 score 44 scripts

thinkr-open

golem:A Framework for Robust Shiny Applications

An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.

Maintained by Colin Fay. Last updated 7 months ago.

golemverse hacktoberfest shiny shiny-apps shiny-r shinyapps

2.0 match 921 stars 14.23 score 167 scripts 62 dependents

bioc

LACE:Longitudinal Analysis of Cancer Evolution (LACE)

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

Maintained by Davide Maspero. Last updated 2 days ago.

biomedicalinformatics singlecell somaticmutation

3.7 match 15 stars 7.75 score 3 scripts

r-lib

lintr:A 'Linter' for R Code

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.

Maintained by Michael Chirico. Last updated 9 days ago.

linter

1.7 match 1.2k stars 17.00 score 916 scripts 33 dependents

workflowr

workflowr:A Framework for Reproducible and Collaborative Data Science

Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.

Maintained by John Blischak. Last updated 4 months ago.

git project-management rmarkdown website workflow

2.4 match 845 stars 11.83 score 566 scripts

openanalytics

inTextSummaryTable:Creation of in-Text Summary Table

Creation of tables of summary statistics or counts for clinical data (for 'TLFs'). These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report (Word format) or a 'topline' presentation (PowerPoint format), or as interactive table (with the 'DT' package) to an html document for clinical data review.

Maintained by Laure Cougnaud. Last updated 9 months ago.

5.1 match 1 stars 5.52 score 47 scripts

statnet

tergm:Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models

An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.

Maintained by Pavel N. Krivitsky. Last updated 4 months ago.

3.0 match 27 stars 9.29 score 78 scripts 3 dependents

jpgattuso

seacarb:Seawater Carbonate Chemistry

Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.

Maintained by Jean-Pierre Gattuso. Last updated 1 years ago.

3.3 match 8 stars 8.27 score 350 scripts 5 dependents

femiguez

nlraa:Nonlinear Regression for Agricultural Applications

Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty eight (28) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses 'nlsLM' for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package provides functions for conducting simulations for 'nlme' and 'gnls' objects as well as bootstrapping. These functions are intended to work with the modeling framework of the 'nlme' package. It also provides four vignettes with extended examples.

Maintained by Fernando Miguez. Last updated 10 months ago.

agricultural ecology nonlinear-mixed-models nonlinear-regression

3.3 match 23 stars 8.19 score 112 scripts 2 dependents

aphalo

photobiology:Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 3 days ago.

light photobiology quantification r4photobiology-suite radiation spectra sun-position

2.9 match 4 stars 9.35 score 604 scripts 12 dependents

richardli

surveyPrev:Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.

Maintained by Qianyu Dong. Last updated 5 days ago.

4.7 match 1 stars 5.76 score 11 scripts

mfasiolo

mgcViz:Visualisations for Generalized Additive Models

Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.

Maintained by Matteo Fasiolo. Last updated 7 months ago.

2.9 match 77 stars 9.38 score 1000 scripts

azure

AzureAuth:Authentication Services for Azure Active Directory

Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.

Maintained by Hong Ooi. Last updated 3 years ago.

azure azure-active-directory azure-sdk-r oauth2

2.6 match 44 stars 10.42 score 57 scripts 23 dependents

jonathan-g

datafsm:Estimating Finite State Machine Models from Data

Automatic generation of finite state machine models of dynamic decision-making that both have strong predictive power and are interpretable in human terms. We use an efficient model representation and a genetic algorithm-based estimation process to generate simple deterministic approximations that explain most of the structure of complex stochastic processes. We have applied the software to empirical data, and demonstrated it's ability to recover known data-generating processes by simulating data with agent-based models and correctly deriving the underlying decision models for multiple agent models and degrees of stochasticity.

Maintained by Jonathan M. Gilligan. Last updated 4 years ago.

machine-learning cpp

4.9 match 11 stars 5.52 score 30 scripts

cjvanlissa

worcs:Workflow for Open Reproducible Code in Science

Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.

Maintained by Caspar J. Van Lissa. Last updated 11 days ago.

2.9 match 83 stars 9.26 score 59 scripts

lbbe-software

rbioacc:Inference and Prediction of ToxicoKinetic (TK) Models

The MOSAICbioacc application is a turnkey package providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.

Maintained by Virgile Baudrot. Last updated 1 years ago.

cpp

5.7 match 4.78 score 8 scripts

nickreich

coarseDataTools:Analysis of Coarsely Observed Data

Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.

Maintained by Nicholas G. Reich. Last updated 2 years ago.

3.3 match 9 stars 8.07 score 37 scripts 8 dependents

tongzhou2017

itol.toolkit:Helper Functions for 'Interactive Tree Of Life'

The 'Interactive Tree Of Life' <https://itol.embl.de/> online server can edit and annotate trees interactively. The 'itol.toolkit' package can support all types of annotation templates.

Maintained by Tong Zhou. Last updated 3 months ago.

bioinformatics itol visualization

3.5 match 167 stars 7.48 score 60 scripts

mjlajeunesse

metagear:Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis

Functionalities for facilitating systematic reviews, data extractions, and meta-analyses. It includes a GUI (graphical user interface) to help screen the abstracts and titles of bibliographic data; tools to assign screening effort across multiple collaborators/reviewers and to assess inter- reviewer reliability; tools to help automate the download and retrieval of journal PDF articles from online databases; figure and image extractions from PDFs; web scraping of citations; automated and manual data extraction from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random effects sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g., effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software (i.e., metawin). Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031. CITE: Lajeunesse, M.J. (2016) Facilitating systematic reviews, data extraction and meta-analysis with the metagear package for R. Methods in Ecology and Evolution 7, 323-330 <doi:10.1111/2041-210X.12472>.

Maintained by Marc J. Lajeunesse. Last updated 4 years ago.

3.9 match 14 stars 6.71 score 91 scripts

mikejareds

hermiter:Efficient Sequential and Batch Estimation of Univariate and Bivariate Probability Density Functions and Cumulative Distribution Functions along with Quantiles (Univariate) and Nonparametric Correlation (Bivariate)

Facilitates estimation of full univariate and bivariate probability density functions and cumulative distribution functions along with full quantile functions (univariate) and nonparametric correlation (bivariate) using Hermite series based estimators. These estimators are particularly useful in the sequential setting (both stationary and non-stationary) and one-pass batch estimation setting for large data sets. Based on: Stephanou, Michael, Varughese, Melvin and Macdonald, Iain. "Sequential quantiles via Hermite series density estimation." Electronic Journal of Statistics 11.1 (2017): 570-607 <doi:10.1214/17-EJS1245>, Stephanou, Michael and Varughese, Melvin. "On the properties of Hermite series based distribution function estimators." Metrika (2020) <doi:10.1007/s00184-020-00785-z> and Stephanou, Michael and Varughese, Melvin. "Sequential estimation of Spearman rank correlation using Hermite series estimators." Journal of Multivariate Analysis (2021) <doi:10.1016/j.jmva.2021.104783>.

Maintained by Michael Stephanou. Last updated 7 months ago.

cumulative-distribution-function kendall-correlation-coefficient online-algorithms probability-density-function quantile spearman-correlation-coefficient statistics streaming-algorithms streaming-data cpp

4.7 match 15 stars 5.58 score 17 scripts

bioc

MOSim:Multi-Omics Simulation (MOSim)

MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.

Maintained by Sonia Tarazona. Last updated 5 months ago.

software timecourse experimentaldesign rnaseq cpp

3.5 match 9 stars 7.46 score 11 scripts

s3alfisc

fwildclusterboot:Fast Wild Cluster Bootstrap Inference for Linear Models

Implementation of fast algorithms for wild cluster bootstrap inference developed in 'Roodman et al' (2019, 'STATA' Journal, <doi:10.1177/1536867X19830877>) and 'MacKinnon et al' (2022), which makes it feasible to quickly calculate bootstrap test statistics based on a large number of bootstrap draws even for large samples. Multiple bootstrap types as described in 'MacKinnon, Nielsen & Webb' (2022) are supported. Further, 'multiway' clustering, regression weights, bootstrap weights, fixed effects and 'subcluster' bootstrapping are supported. Further, both restricted ('WCR') and unrestricted ('WCU') bootstrap are supported. Methods are provided for a variety of fitted models, including 'lm()', 'feols()' (from package 'fixest') and 'felm()' (from package 'lfe'). Additionally implements a 'heteroskedasticity-robust' ('HC1') wild bootstrap. Last, the package provides an R binding to 'WildBootTests.jl', which provides additional speed gains and functionality, including the 'WRE' bootstrap for instrumental variable models (based on models of type 'ivreg()' from package 'ivreg') and hypotheses with q > 1.

Maintained by Alexander Fischer. Last updated 2 years ago.

clustered-standard-errors linear-regression-models wild-bootstrap wild-cluster-bootstrap openblas cpp openmp

3.9 match 24 stars 6.67 score 109 scripts 2 dependents

bioc

BgeeDB:Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

Maintained by Julien Wollbrett. Last updated 5 months ago.

software dataimport sequencing geneexpression microarray go genesetenrichment bioinformatics enrichment-analysis rna-seq scrna-seq single-cell

3.0 match 15 stars 8.46 score 19 scripts 1 dependents

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 10 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

1.8 match 222 stars 14.71 score 436 scripts 119 dependents

dominiquemaucieri

quadcleanR:Cleanup and Visualization of Quadrat Data

A tool that can be customized to aid in the clean up of ecological data collected using quadrats and can crop quadrats to ensure comparability between quadrats collected under different methodologies.

Maintained by Dominique Maucieri. Last updated 2 years ago.

5.8 match 4.45 score 14 scripts

watanabe-j

qfratio:Moments and Distributions of Ratios of Quadratic Forms Using Recursion

Evaluates moments of ratios (and products) of quadratic forms in normal variables, specifically using recursive algorithms developed by Bao and Kan (2013) <doi:10.1016/j.jmva.2013.03.002> and Hillier et al. (2014) <doi:10.1017/S0266466613000364>. Also provides distribution, quantile, and probability density functions of simple ratios of quadratic forms in normal variables with several algorithms. Originally developed as a supplement to Watanabe (2023) <doi:10.1007/s00285-023-01930-8> for evaluating average evolvability measures in evolutionary quantitative genetics, but can be used for a broader class of statistics. Generating functions for these moments are also closely related to the top-order zonal and invariant polynomials of matrix arguments.

Maintained by Junya Watanabe. Last updated 6 months ago.

quadratic-forms rcpp rcppeigen zonal-polynomials cpp openmp

5.6 match 1 stars 4.60 score 5 scripts

bioc

crlmm:Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

Maintained by Benilton S Carvalho. Last updated 12 days ago.

microarray preprocessing snp copynumbervariation

5.4 match 4.78 score 37 scripts 3 dependents

sparklyr

sparklyr:R Interface to Apache Spark

R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.

Maintained by Edgar Ruiz. Last updated 10 days ago.

apache-spark distributed dplyr ide livy machine-learning remote-clusters spark sparklyr

1.7 match 959 stars 15.16 score 4.0k scripts 21 dependents

rte-antares-rpackage

antaresEditObject:Edit an 'Antares' Simulation

Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.

Maintained by Tatiana Vargas. Last updated 28 days ago.

antares-simulation cluster energy monte-carlo-simulation rte

2.9 match 8 stars 8.76 score 101 scripts

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

1.5 match 1.1k stars 16.96 score 9.2k scripts 111 dependents

pablo14

funModeling:Exploratory Data Analysis and Data Preparation Tool-Box

Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<https://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.

Maintained by Pablo Casas. Last updated 2 years ago.

3.0 match 100 stars 8.57 score 654 scripts

r-forge

Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable

Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.

Maintained by Martin Maechler. Last updated 4 months ago.

mpfr4 gmp

2.3 match 11.30 score 316 scripts 141 dependents

ropensci

rsi:Efficiently Retrieve and Process Satellite Imagery

Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.

Maintained by Michael Mahoney. Last updated 2 months ago.

3.5 match 49 stars 7.20 score 38 scripts

aidanmorales

rTwig:Realistic Quantitative Structure Models

Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.

Maintained by Aidan Morales. Last updated 13 days ago.

forestry lidar modeling qsm rcpp cpp

3.6 match 8 stars 7.10 score 13 scripts

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

3.6 match 145 stars 7.09 score 50 scripts 2 dependents

hneth

riskyr:Rendering Risk Literacy more Transparent

Risk-related information (like the prevalence of conditions, the sensitivity and specificity of diagnostic tests, or the effectiveness of interventions or treatments) can be expressed in terms of frequencies or probabilities. By providing a toolbox of corresponding metrics and representations, 'riskyr' computes, translates, and visualizes risk-related information in a variety of ways. Adopting multiple complementary perspectives provides insights into the interplay between key parameters and renders teaching and training programs on risk literacy more transparent.

Maintained by Hansjoerg Neth. Last updated 10 months ago.

2x2-matrix bayesian-inference contingency-table representation risk risk-literacy visualization

3.4 match 19 stars 7.36 score 80 scripts

statisticsnorway

easySdcTable:Easy Interface to the Statistical Disclosure Control Package 'sdcTable' Extended with Own Implementation of 'GaussSuppression'

The main function, ProtectTable(), performs table suppression according to a frequency rule with a data set as the only required input. Within this function, protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called. Lists of level-hierarchy (parameter 'dimList') and other required input to these functions are created automatically. The suppression method Gauss (default) is implemented independently of 'sdcTable'. The function, PTgui(), starts a graphical user interface based on the 'shiny' package.

Maintained by Øyvind Langsrud. Last updated 2 years ago.

6.0 match 1 stars 4.20 score 16 scripts

tidymodels

dials:Tools for Creating Tuning Parameter Values

Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.

Maintained by Hannah Frick. Last updated 30 days ago.

1.8 match 114 stars 14.31 score 426 scripts 52 dependents

collinerickson

TestFunctions:Test Functions for Simulation Experiments and Evaluating Optimization and Emulation Algorithms

Test functions are often used to test computer code. They are used in optimization to test algorithms and in metamodeling to evaluate model predictions. This package provides test functions that can be used for any purpose.

Maintained by Collin Erickson. Last updated 6 months ago.

4.8 match 5.16 score 48 scripts 2 dependents

bioc

xCell2:A Tool for Generic Cell Type Enrichment Analysis

xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.

Maintained by Almog Angel. Last updated 16 hours ago.

geneexpression transcriptomics microarray rnaseq singlecell differentialexpression immunooncology genesetenrichment

4.0 match 6 stars 6.16 score 15 scripts

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

1.8 match 206 stars 13.73 score 2.2k scripts 123 dependents

bioc

missMethyl:Analysing Illumina HumanMethylation BeadChip Data

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Maintained by Belinda Phipson. Last updated 14 days ago.

normalization dnamethylation methylationarray genomicvariation geneticvariability differentialmethylation genesetenrichment

3.4 match 7.24 score 300 scripts 1 dependents

drg-123

NSM3:Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition

Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.

Maintained by Grant Schneider. Last updated 4 months ago.

6.5 match 1 stars 3.77 score 115 scripts 1 dependents