Showing 74 of total 74 results (show query)
koalaverse
sure:Surrogate Residuals for Ordinal and General Regression Models
An implementation of the surrogate approach to residuals and diagnostics for ordinal and general regression models; for details, see Liu and Zhang (2017, <doi:https://doi.org/10.1080/01621459.2017.1292915>) and Greenwell et al. (2017, <https://journal.r-project.org/archive/2018/RJ-2018-004/index.html>). These residuals can be used to construct standard residual plots for model diagnostics (e.g., residual-vs-fitted value plots, residual-vs-covariate plots, Q-Q plots, etc.). The package also provides an 'autoplot' function for producing standard diagnostic plots using 'ggplot2' graphics. The package currently supports cumulative link models from packages 'MASS', 'ordinal', 'rms', and 'VGAM'. Support for binary regression models using the standard 'glm' function is also available.
Maintained by Brandon Greenwell. Last updated 15 days ago.
categorical-datadiagnosticsordinal-regressionresiduals
56.6 match 9 stars 5.58 score 47 scripts 1 dependents
colinfay
attempt:Tools for Defensive Programming
Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.
Maintained by Colin Fay. Last updated 7 months ago.
8.0 match 126 stars 11.57 score 101 scripts 86 dependents
icasas
tvReg:Time-Varying Coefficient for Single and Multi-Equation Regressions
Fitting time-varying coefficient models for single and multi-equation regressions, using kernel smoothing techniques.
Maintained by Isabel Casas. Last updated 2 years ago.
autoregressivenonparametricregressionsurevectorautoregressive
11.0 match 19 stars 6.25 score 62 scripts
paterijk
MCDA:Support for the Multicriteria Decision Aiding Process
Support for the analyst in a Multicriteria Decision Aiding (MCDA) process with algorithms, preference elicitation and data visualisation functions. Sébastien Bigaret, Richard Hodgett, Patrick Meyer, Tatyana Mironova, Alexandru Olteanu (2017) Supporting the multi-criteria decision aiding process : R and the MCDA package, Euro Journal On Decision Processes, Volume 5, Issue 1 - 4, pages 169 - 194 <doi:10.1007/s40070-017-0064-1>.
Maintained by Patrick Meyer. Last updated 2 years ago.
6.9 match 30 stars 6.04 score 182 scripts
cran
wavethresh:Wavelets Statistics and Transforms
Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Maintained by Guy Nason. Last updated 7 months ago.
6.9 match 5.89 score 41 dependents
trambakbanerjee
asus:Adaptive SURE Thresholding Using Side Information
Provides the ASUS procedure for estimating a high dimensional sparse parameter in the presence of auxiliary data that encode side information on sparsity. It is a robust data combination procedure in the sense that even when pooling non-informative auxiliary data ASUS would be at least as efficient as competing soft thresholding based methods that do not use auxiliary data. For more information, please see the paper Adaptive Sparse Estimation with Side Information by Banerjee, Mukherjee and Sun (JASA 2020).
Maintained by Trambak Banerjee. Last updated 2 years ago.
9.0 match 3 stars 4.29 score 13 scripts
olink-proteomics
OlinkAnalyze:Facilitate Analysis of Proteomic Data from Olink
A collection of functions to facilitate analysis of proteomic data from Olink, primarily NPX data that has been exported from Olink Software. The functions also work on QUANT data from Olink by log- transforming the QUANT data. The functions are focused on reading data, facilitating data wrangling and quality control analysis, performing statistical analysis and generating figures to visualize the results of the statistical analysis. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
Maintained by Kathleen Nevola. Last updated 21 days ago.
olinkproteomicsproteomics-data-analysis
3.1 match 104 stars 9.72 score 61 scripts
joshuaulrich
TTR:Technical Trading Rules
A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.
Maintained by Joshua Ulrich. Last updated 1 years ago.
algorithmic-tradingfinancetechnical-analysis
2.0 match 338 stars 15.11 score 2.8k scripts 359 dependents
hugogogo
sprintr:Sparse Reluctant Interaction Modeling
An implementation of a computationally efficient method to fit large-scale interaction models based on the reluctant interaction selection principle. The method and its properties are described in greater depth in Yu, G., Bien, J., and Tibshirani, R.J. (2019) "Reluctant interaction modeling", which is available at <arXiv:1907.08414>.
Maintained by Guo Yu. Last updated 3 years ago.
5.3 match 3 stars 4.18 score 7 scripts
bnosac
udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Maintained by Jan Wijffels. Last updated 2 years ago.
conlldependency-parserlemmatizationnatural-language-processingnlppos-taggingr-pkgrcpptext-miningtokenizerudpipecpp
1.7 match 215 stars 11.83 score 1.2k scripts 9 dependents
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
2.0 match 19 stars 9.55 score 155 scripts 2 dependents
darwin-eu
CDMConnector:Connect to an OMOP Common Data Model
Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.
Maintained by Adam Black. Last updated 20 days ago.
1.6 match 12 stars 11.39 score 502 scripts 12 dependents
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.
2.3 match 3 stars 7.88 score 108 scripts 23 dependents
fabnavarro
rwavelet:Wavelet Analysis
Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholding, block thresholding, linear,...) with applications to data compression, denoising/regression or clustering. The core of the code is a port of 'MATLAB' Wavelab toolbox written by D. Donoho, A. Maleki and M. Shahram (<https://statweb.stanford.edu/~wavelab/>).
Maintained by Navarro Fabien. Last updated 7 months ago.
machine-learningregressionwavelet
3.5 match 5 stars 5.01 score 41 scripts
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 20 days ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
1.8 match 126 stars 9.90 score 226 scripts 2 dependentsdarwin-eu
omopgenerics:Methods and Classes for the OMOP Common Data Model
Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.
Maintained by Martí Català. Last updated 11 days ago.
1.7 match 9.97 score 193 scripts 16 dependentsbioc
mspms:Tools for the analysis of MSP-MS data
This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.
Maintained by Charlie Bayne. Last updated 4 months ago.
proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis
3.3 match 4.95 score 4 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-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport
1.6 match 42 stars 9.35 score 105 scripts 1 dependents
insightsengineering
teal.transform:Functions for Extracting and Merging Data in the 'teal' Framework
A standardized user interface for column selection, that facilitates dataset merging in 'teal' framework.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
1.8 match 3 stars 8.39 score 9 scripts 4 dependentsbioc
monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
Maintained by Cole Trapnell. Last updated 5 months ago.
immunooncologysequencingrnaseqgeneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationclusteringmultiplecomparisonqualitycontrolcpp
1.6 match 8.89 score 1.6k scripts 2 dependents
kwb-r
kwb.utils:General Utility Functions Developed at KWB
This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).
Maintained by Hauke Sonnenberg. Last updated 12 months ago.
1.8 match 8 stars 7.33 score 12 scripts 78 dependents
ewenharrison
finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling
Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Maintained by Ewen Harrison. Last updated 7 months ago.
1.1 match 270 stars 11.43 score 1.0k scripts
inbo
checklist:A Thorough and Strict Set of Checks for R Packages and Source Code
An opinionated set of rules for R packages and R source code projects.
Maintained by Thierry Onkelinx. Last updated 28 days ago.
checklistcontinuous-integrationcontinuous-testingquality-assurance
1.7 match 19 stars 7.24 score 21 scripts 2 dependents
silentspringinstitute
RNHANES:Facilitates Analysis of CDC NHANES Data
Tools for downloading and analyzing CDC NHANES data, with a focus on analytical laboratory data.
Maintained by Herb Susmann. Last updated 3 days ago.
1.6 match 77 stars 7.58 score 83 scriptsbioc
GenomicDistributions:GenomicDistributions: fast analysis of genomic intervals with Bioconductor
If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.
Maintained by Kristyna Kupkova. Last updated 5 months ago.
softwaregenomeannotationgenomeassemblydatarepresentationsequencingcoveragefunctionalgenomicsvisualization
1.6 match 26 stars 7.44 score 25 scriptscran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
3.4 match 2 stars 3.48 score
pecanproject
PEcAn.dvmdostem:PEcAn Package for Integration of the Dvmdostem Model
This module provides functions to link the dvmdostem model to PEcAn.
Maintained by Tobey Carman. Last updated 3 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
1.5 match 216 stars 7.56 score 3 scripts
ohdsi
PatientLevelPrediction:Develop Clinical Prediction Models Using the Common Data Model
A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Maintained by Egill Fridgeirsson. Last updated 10 days ago.
1.1 match 190 stars 10.85 score 297 scripts
lorenzwalthert
precommit:Pre-Commit Hooks
Useful git hooks for R building on top of the multi-language framework 'pre-commit' for hook management. This package provides git hooks for common tasks like formatting files with 'styler' or spell checking as well as wrapper functions to access the 'pre-commit' executable.
Maintained by Lorenz Walthert. Last updated 1 days ago.
1.2 match 257 stars 9.72 score 10 scripts
shaelebrown
TDApplied:Machine Learning and Inference for Topological Data Analysis
Topological data analysis is a powerful tool for finding non-linear global structure in whole datasets. The main tool of topological data analysis is persistent homology, which computes a topological shape descriptor of a dataset called a persistence diagram. 'TDApplied' provides useful and efficient methods for analyzing groups of persistence diagrams with machine learning and statistical inference, and these functions can also interface with other data science packages to form flexible and integrated topological data analysis pipelines.
Maintained by Shael Brown. Last updated 5 months ago.
1.7 match 16 stars 6.60 score 8 scripts
r-lib
liteq:Lightweight Portable Message Queue Using 'SQLite'
Temporary and permanent message queues for R. Built on top of 'SQLite' databases. 'SQLite' provides locking, and makes it possible to detect crashed consumers. Crashed jobs can be automatically marked as "failed", or put in the queue again, potentially a limited number of times.
Maintained by Gábor Csárdi. Last updated 4 months ago.
1.9 match 57 stars 5.91 score 19 scripts 1 dependentsbioc
rcellminer:rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.
Maintained by Augustin Luna. Last updated 5 months ago.
acghcellbasedassayscopynumbervariationgeneexpressionpharmacogenomicspharmacogeneticsmirnacheminformaticsvisualizationsoftwaresystemsbiology
1.9 match 5.71 score 113 scripts
pik-piam
piamInterfaces:Project specific interfaces to REMIND / MAgPIE
Project specific interfaces to REMIND / MAgPIE.
Maintained by Falk Benke. Last updated 14 hours ago.
1.6 match 6.64 score 38 scripts 7 dependents
learnitr
learnitgrid:Manage Rubrics or Assessment Grids for GitHub Repositories
Create and manage semi-automatically rubrics to assess GitHub projects (R scripts, R Markdown or Quarto files). Create directed projects where students have to complete documents and submit them to GitHub (classroom) so that they are evaluated using the rubric (or assessment grid).
Maintained by Philippe Grosjean. Last updated 9 months ago.
3.5 match 1 stars 3.00 score 7 scripts
terminological
ggrrr:Addressing Annoyances and Irritations
Visualisation hacks, tabular data helpers, fonts, caching, tidy data functions. It is an swiss army knife, jack of all trades.
Maintained by Robert Challen. Last updated 9 months ago.
3.5 match 1 stars 2.74 score 11 scripts
ramiromagno
gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.
Maintained by Ramiro Magno. Last updated 1 years ago.
thirdpartyclientbiomedicalinformaticsgenomewideassociationsnpassociation-studiesgwas-cataloghumanrest-clienttraittrait-ontology
1.1 match 95 stars 8.10 score 49 scripts 1 dependents
ravingmantis
unittest:TAP-Compliant Unit Testing
Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Maintained by Jamie Lentin. Last updated 7 months ago.
1.2 match 4 stars 7.43 score 224 scripts
nschiett
fishualize:Color Palettes Based on Fish Species
Implementation of color palettes based on fish species.
Maintained by Nina M. D. Schiettekatte. Last updated 11 months ago.
1.0 match 155 stars 8.54 score 370 scripts
yhat
yhatr:R Binder for the Yhat API
Deploy, maintain, and invoke models via the Yhat REST API.
Maintained by Greg Lamp. Last updated 8 years ago.
1.8 match 16 stars 4.87 score 58 scripts
xuejunma
QCSIS:Sure Independence Screening via Quantile Correlation and Composite Quantile Correlation
Quantile correlation-sure independence screening (QC-SIS) and composite quantile correlation-sure independence screening (CQC-SIS) for ultrahigh-dimensional data.
Maintained by Xuejun Ma. Last updated 9 years ago.
8.7 match 1.00 score 5 scripts
jmzobitz
neonSoilFlux:Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites
Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.
Maintained by John Zobitz. Last updated 10 months ago.
1.6 match 6 stars 5.43 score 2 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
3.6 match 2.28 score 38 scripts
rdinnager
slimr:Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations
Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.
Maintained by Russell Dinnage. Last updated 4 months ago.
1.7 match 8 stars 4.70 score 42 scripts
papatheodorou-group
scOntoMatch:Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'
Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.
Maintained by Yuyao Song. Last updated 1 years ago.
1.6 match 7 stars 4.54 score 6 scripts
miracum
DIZtools:Lightweight Utilities for 'DIZ' R Package Development
Lightweight utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 1 years ago.
1.8 match 3 stars 4.13 score 2 scripts 3 dependentsbioc
surfaltr:Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.
Maintained by Pooja Gangras. Last updated 5 months ago.
softwarevisualizationdatarepresentationsplicedalignmentalignmentmultiplesequencealignmentmultiplecomparison
1.7 match 4.00 score 2 scripts
ropensci
tidyqpcr:Quantitative PCR Analysis with the Tidyverse
For reproducible quantitative PCR (qPCR) analysis building on packages from the ’tidyverse’, notably ’dplyr’ and ’ggplot2’. It normalizes (by ddCq), summarizes, and plots pre-calculated Cq data, and plots raw amplification and melt curves from Roche Lightcycler (tm) machines. It does NOT (yet) calculate Cq data from amplification curves.
Maintained by Edward Wallace. Last updated 11 months ago.
miqeqpcrqpcr-analysistidyverse
1.2 match 54 stars 5.64 score 20 scripts
desanou
mglasso:Multiscale Graphical Lasso
Inference of Multiscale graphical models with neighborhood selection approach. The method is based on solving a convex optimization problem combining a Lasso and fused-group Lasso penalties. This allows to infer simultaneously a conditional independence graph and a clustering partition. The optimization is based on the Continuation with Nesterov smoothing in a Shrinkage-Thresholding Algorithm solver (Hadj-Selem et al. 2018) <doi:10.1109/TMI.2018.2829802> implemented in python.
Maintained by Edmond Sanou. Last updated 2 years ago.
1.6 match 2 stars 4.11 score 13 scripts
jmcurran
relSim:Relative Simulator
A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Maintained by James M. Curran. Last updated 1 years ago.
2.0 match 3.18 score 30 scripts
wencanhong
cdcsis:Conditional Distance Correlation Based Feature Screening and Conditional Independence Inference
Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <https://www3.stat.sinica.edu.tw/statistica/J28N1/J28N114/J28N114.html>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.
Maintained by Canhong Wen. Last updated 7 months ago.
2.2 match 1 stars 2.88 score 25 scripts 1 dependents
rameshram96
visvaR:Shiny-Based Statistical Solutions for Agricultural Research
Visualize Variance is an intuitive 'shiny' applications tailored for agricultural research data analysis, including one-way and two-way analysis of variance, correlation, and other essential statistical tools. Users can easily upload their datasets, perform analyses, and download the results as a well-formatted document, streamlining the process of data analysis and reporting in agricultural research.The experimental design methods are based on classical work by Fisher (1925) and Scheffe (1959). The correlation visualization approaches follow methods developed by Wei & Simko (2021) and Friendly (2002) <doi:10.1198/000313002533>.
Maintained by Ramesh Ramasamy. Last updated 4 months ago.
agricultureanova-analysiscorrelationexperexperimentalexperimental-design
1.7 match 3.54 score 6 scripts
lmullen
gender:Predict Gender from Names Using Historical Data
Infers state-recorded gender categories from first names and dates of birth using historical datasets. By using these datasets instead of lists of male and female names, this package is able to more accurately infer the gender of a name, and it is able to report the probability that a name was male or female. GUIDELINES: This method must be used cautiously and responsibly. Please be sure to see the guidelines and warnings about usage in the 'README' or the package documentation. See Blevins and Mullen (2015) <http://www.digitalhumanities.org/dhq/vol/9/3/000223/000223.html>.
Maintained by Lincoln Mullen. Last updated 3 years ago.
0.5 match 189 stars 9.80 score 265 scripts 7 dependents
lionel-
fontquiver:Set of Installed Fonts
Provides a set of fonts with permissive licences. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.
Maintained by Lionel Henry. Last updated 6 years ago.
0.5 match 17 stars 8.73 score 14 scripts 147 dependentscran
TSGSIS:Two Stage-Grouped Sure Independence Screening
To provide a high dimensional grouped variable selection approach for detection of whole-genome SNP effects and SNP-SNP interactions, as described in Fang et al. (2017, under review).
Maintained by Yao-Hwei Fang. Last updated 8 years ago.
4.7 match 1 stars 1.00 score
statjs
bspcov:Bayesian Sparse Estimation of a Covariance Matrix
Provides functions which perform Bayesian estimations of a covariance matrix for multivariate normal data. Assumes that the covariance matrix is sparse or band matrix and positive-definite. This software has been developed using funding supported by Basic Science Research Program through the National Research Foundation of Korea ('NRF') funded by the Ministry of Education ('RS-2023-00211979', 'NRF-2022R1A5A7033499', 'NRF-2020R1A4A1018207' and 'NRF-2020R1C1C1A01013338').
Maintained by Kyeongwon Lee. Last updated 4 months ago.
1.7 match 1 stars 2.70 score 3 scriptscran
crosstalkr:Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks
Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.
Maintained by Davis Weaver. Last updated 10 months ago.
1.7 match 2.70 score
drjohanlk
kollaR:Filtering, Visualization and Analysis of Eye Tracking Data
Functions for analysing eye tracking data, including event detection (I-VT, I-DT and two means clustering), visualizations and area of interest (AOI) based analyses. See separate documentation for each function. The principles underlying I-VT and I-DT filters are described in Salvucci & Goldberg (2000,\doi{10.1145/355017.355028}). Two-means clustering is described in Hessels et al. (2017, \doi{10.3758/s13428-016-0822-1}).
Maintained by Johan Lundin Kleberg. Last updated 25 days ago.
3.0 match 1.30 score
ppbds
r4ds.tutorials:Tutorials for "R for Data Science"
When assigned "R for Data Science" (Wickham, Çetinkaya-Rundel, and Grolemund (2023, ISBN: 1492097402)), students should read the book and type in all the associated R commands themselves. Sadly, that never happens. These tutorials allow students to demonstrate (and their instructors to be sure) that all work has been completed. See Kane (2023) <https://ppbds.github.io/tutorial.helpers/articles/instructions.html> from the 'tutorial.helpers' package for a background discussion.
Maintained by David Kane. Last updated 22 days ago.
0.5 match 8 stars 6.59 score 11 scripts
ai4ci
interfacer:Define and Enforce Contracts for Dataframes as Function Parameters
A dataframe validation framework for package builders who use dataframes as function parameters. It performs checks on column names, coerces data-types, and checks grouping to make sure user inputs conform to a specification provided by the package author. It provides a mechanism for package authors to automatically document supported dataframe inputs and selectively dispatch to functions depending on the format of a dataframe much like S3 does for classes. It also contains some developer tools to make working with and documenting dataframe specifications easier. It helps package developers to improve their documentation and simplifies parameter validation where dataframes are used as function parameters.
Maintained by Robert Challen. Last updated 1 months ago.
0.5 match 2 stars 6.43 score 2 dependents
thomasp85
routr:A Simple Router for HTTP and WebSocket Requests
In order to make sure that web request ends up in the correct handler function a router is often used. 'routr' is a package implementing a simple but powerful routing functionality for R based servers. It is a fully functional 'fiery' plugin, but can also be used with other 'httpuv' based servers.
Maintained by Thomas Lin Pedersen. Last updated 19 hours ago.
http-routermiddlewarerouterwebtechnology
0.5 match 56 stars 6.23 score 25 scriptsinsightsengineering
ggplot2.utils:Selected Utilities Extending 'ggplot2'
Selected utilities, in particular 'geoms' and 'stats' functions, extending the 'ggplot2' package. This package imports functions from 'EnvStats' <doi:10.1007/978-1-4614-8456-1> by Millard (2013), 'ggpp' <https://CRAN.R-project.org/package=ggpp> by Aphalo et al. (2023) and 'ggstats' <doi:10.5281/zenodo.10183964> by Larmarange (2023), and then exports them. This package also contains modified code from 'ggquickeda' <https://CRAN.R-project.org/package=ggquickeda> by Mouksassi et al. (2023) for Kaplan-Meier lines and ticks additions to plots. All functions are tested to make sure that they work reliably.
Maintained by Daniel Sabanés Bové. Last updated 9 months ago.
0.5 match 6 stars 6.26 score 14 scripts
evanbiederstedt
Rook:HTTP Web Server for R
An HTTP web server for R with a documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications. To get started, be sure and read the 'Rook' help file first.
Maintained by Evan Biederstedt. Last updated 2 years ago.
0.5 match 1 stars 5.54 score 109 scripts 3 dependents
magichead99
bread:Analyze Big Files Without Loading Them in Memory
A simple set of wrapper functions for data.table::fread() that allows subsetting or filtering rows and selecting columns of table-formatted files too large for the available RAM. 'b stands for 'big files'. bread makes heavy use of Unix commands like 'grep', 'sed', 'wc', 'awk' and 'cut'. They are available by default in all Unix environments. For Windows, you need to install those commands externally in order to simulate a Unix environment and make sure that the executables are in the Windows PATH variable. To my knowledge, the simplest ways are to install 'RTools', 'Git' or 'Cygwin'. If they have been correctly installed (with the expected registry entries), they should be detected on loading the package and the correct directories will be added automatically to the PATH.
Maintained by Vincent Guegan. Last updated 2 years ago.
0.5 match 14 stars 5.37 score 56 scripts 2 dependents
edelmand21
dcortools:Providing Fast and Flexible Functions for Distance Correlation Analysis
Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <arXiv:1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Maintained by Dominic Edelmann. Last updated 2 years ago.
1.6 match 1.70 scorebioc
seahtrue:Seahtrue revives XF data for structured data analysis
Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.
Maintained by Vincent de Boer. Last updated 5 months ago.
cellbasedassaysfunctionalpredictiondatarepresentationdataimportcellbiologycheminformaticsmetabolomicsmicrotitreplateassayvisualizationqualitycontrolbatcheffectexperimentaldesignpreprocessinggo
0.5 match 5.04 score 2 scripts
yufeng031
bestridge:A Comprehensive R Package for Best Subset Selection
The bestridge package is designed to provide a one-stand service for users to successfully carry out best ridge regression in various complex situations via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. This package allows users to perform the regression, classification, count regression and censored regression for (ultra) high dimensional data, and it also supports advanced usages like group variable selection and nuisance variable selection.
Maintained by Liyuan Hu. Last updated 3 years ago.
1.2 match 2.00 score 6 scripts
theeliteanalyst
Riex:IEX Stocks and Market Data
Retrieves efficiently and reliably Investors Exchange ('IEX') stock and market data using 'IEX Cloud API'. The platform is offered by Investors Exchange Group (IEX Group). Main goal is to leverage 'R' capabilities including existing packages to effectively provide financial and statistical analysis as well as visualization in support of fact-based decisions. In addition, continuously improve and enhance 'Riex' by applying best practices and being in tune with users' feedback and requirements. Please, make sure to review and acknowledge Investors Exchange Group (IEX Group) terms and conditions before using 'Riex' (<https://iexcloud.io/terms/>).
Maintained by Myriam Ibrahim. Last updated 4 years ago.
financefinancial-analysisfinancial-dataiexiex-apiiexcloud
0.5 match 9 stars 4.69 score 11 scriptscran
GWASinspector:Comprehensive and Easy to Use Quality Control of GWAS Results
When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Maintained by Alireza Ani. Last updated 11 months ago.
1.1 match 2.00 score
lafaye
ConvergenceConcepts:Seeing Convergence Concepts in Action
This is a pedagogical package, designed to help students understanding convergence of random variables. It provides a way to investigate interactively various modes of convergence (in probability, almost surely, in law and in mean) of a sequence of i.i.d. random variables. Visualisation of simulated sample paths is possible through interactive plots. The approach is illustrated by examples and exercises through the function 'investigate', as described in Lafaye de Micheaux and Liquet (2009) <doi:10.1198/tas.2009.0032>. The user can study his/her own sequences of random variables.
Maintained by Pierre Lafaye De Micheaux. Last updated 3 years ago.
2.3 match 1.00 score 10 scripts
cran
stockR:Identifying Stocks in Genetic Data
Provides a mixture model for clustering individuals (or sampling groups) into stocks based on their genetic profile. Here, sampling groups are individuals that are sure to come from the same stock (e.g. breeding adults or larvae). The mixture (log-)likelihood is maximised using the EM-algorithm after finding good starting values via a K-means clustering of the genetic data. Details can be found in: Foster, S. D.; Feutry, P.; Grewe, P. M.; Berry, O.; Hui, F. K. C. & Davies (2020) <doi:10.1111/1755-0998.12920>.
Maintained by Scott D. Foster. Last updated 2 years ago.
0.5 match 2.00 score