R-universe search: wrapper

ivwalle

checkarg:Check the Basic Validity of a (Function) Argument

Utility functions that allow checking the basic validity of a function argument or any other value, including generating an error and assigning a default in a single line of code. The main purpose of the package is to provide simple and easily readable argument checking to improve code robustness.

Maintained by Ivo Van Walle. Last updated 7 years ago.

747.4 match 3.61 score 404 scripts

elbersb

tidylog:Logging for 'dplyr' and 'tidyr' Functions

Provides feedback about 'dplyr' and 'tidyr' operations.

Maintained by Benjamin Elbers. Last updated 9 months ago.

dplyr tidyr tidyverse wrapper-functions

127.5 match 593 stars 10.23 score 1.7k scripts

ecpolley

SuperLearner:Super Learner Prediction

Implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.

Maintained by Eric Polley. Last updated 1 years ago.

39.6 match 274 stars 12.85 score 2.1k scripts 36 dependents

berndbischl

BBmisc:Miscellaneous Helper Functions for B. Bischl

Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.

Maintained by Bernd Bischl. Last updated 2 years ago.

26.5 match 20 stars 10.59 score 980 scripts 69 dependents

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 1 months ago.

docx html5 ms-office-documents rmarkdown table

15.3 match 583 stars 17.04 score 7.3k scripts 119 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.

19.8 match 270 stars 11.43 score 1.0k scripts

bioc

DAPAR:Tools for the Differential Analysis of Proteins Abundance with R

The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

Maintained by Samuel Wieczorek. Last updated 5 months ago.

proteomics normalization preprocessing massspectrometry qualitycontrol go dataimport prostar1

39.9 match 2 stars 5.42 score 22 scripts 1 dependents

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

14.9 match 725 stars 13.93 score 4.9k scripts 18 dependents

braverock

PerformanceAnalytics:Econometric Tools for Performance and Risk Analysis

Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

Maintained by Brian G. Peterson. Last updated 3 months ago.

12.6 match 222 stars 15.93 score 4.8k scripts 20 dependents

triadsou

RcmdrPlugin.KMggplot2:R Commander Plug-in for Data Visualization with 'ggplot2'

A GUI front-end for 'ggplot2' supports Kaplan-Meier plot, histogram, Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart, bar chart, contour plot, and distribution plot.

Maintained by Triad sou.. Last updated 5 years ago.

55.1 match 3.18 score 8 scripts

bioc

mixOmics:Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Maintained by Eva Hamrud. Last updated 3 days ago.

immunooncology microarray sequencing metabolomics metagenomics proteomics geneprediction multiplecomparison classification regression bioconductor genomics genomics-data genomics-visualization multivariate-analysis multivariate-statistics omics r-pkg r-project

11.9 match 182 stars 13.71 score 1.3k scripts 22 dependents

kylebutts

shiny.tailwind:'TailwindCSS' for Shiny Apps

Allows 'TailwindCSS' to be used in Shiny apps with just-in-time compiling, custom css with '@apply' directive, and custom tailwind configurations.

Maintained by Kyle Butts. Last updated 5 days ago.

22.3 match 59 stars 6.82 score 28 scripts

danforthcenter

pcvr:Plant Phenotyping and Bayesian Statistics

Analyse common types of plant phenotyping data, provide a simplified interface to longitudinal growth modeling and select Bayesian statistics, and streamline use of 'PlantCV' output. Several Bayesian methods and reporting guidelines for Bayesian methods are described in Kruschke (2018) <doi:10.1177/2515245918771304>, Kruschke (2013) <doi:10.1037/a0029146>, and Kruschke (2021) <doi:10.1038/s41562-021-01177-7>.

Maintained by Josh Sumner. Last updated 4 days ago.

21.6 match 4 stars 6.99 score 39 scripts

juliasilge

tidytext:Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools

Using tidy data principles can make many text mining tasks easier, more effective, and consistent with tools already in wide use. Much of the infrastructure needed for text mining with tidy data frames already exists in packages like 'dplyr', 'broom', 'tidyr', and 'ggplot2'. In this package, we provide functions and supporting data sets to allow conversion of text to and from tidy formats, and to switch seamlessly between tidy tools and existing text mining packages.

Maintained by Julia Silge. Last updated 11 months ago.

natural-language-processing text-mining tidy-data tidyverse

8.8 match 1.2k stars 16.86 score 17k scripts 61 dependents

sbfnk

rbi:Interface to 'LibBi'

Provides a complete interface to 'LibBi', a library for Bayesian inference (see <https://libbi.org> and Murray, 2015 <doi:10.18637/jss.v067.i10> for more information). This includes functions for manipulating 'LibBi' models, for reading and writing 'LibBi' input/output files, for converting 'LibBi' output to provide traces for use with the coda package, and for running 'LibBi' to conduct inference.

Maintained by Sebastian Funk. Last updated 10 months ago.

17.2 match 24 stars 8.35 score 390 scripts 1 dependents

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Maintained by Yihui Xie. Last updated 1 days ago.

dynamic-documents knitr literate-programming rmarkdown sweave

5.8 match 2.4k stars 23.62 score 116k scripts 4.2k dependents

bioc

YAPSA:Yet Another Package for Signature Analysis

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

Maintained by Zuguang Gu. Last updated 5 months ago.

sequencing dnaseq somaticmutation visualization clustering genomicvariation statisticalmethod biologicalquestion

20.6 match 6.41 score 57 scripts

bioc

scone:Single Cell Overview of Normalized Expression data

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

Maintained by Davide Risso. Last updated 25 days ago.

immunooncology normalization preprocessing qualitycontrol geneexpression rnaseq software transcriptomics sequencing singlecell coverage

14.2 match 53 stars 9.12 score 104 scripts

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 12 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

9.2 match 274 stars 13.63 score 1.6k scripts 23 dependents

muschellij2

fslr:Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Wrapper functions that interface with 'FSL' <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

Maintained by John Muschelli. Last updated 1 months ago.

fsl fslr neuroimaging neuroimaging-analysis neuroimaging-data-science

14.6 match 41 stars 8.01 score 420 scripts

dheerajagarwal

rgdax:Wrapper for 'Coinbase Pro (erstwhile GDAX)' Cryptocurrency Exchange

Allow access to both public and private end points to Coinbase Pro (erstwhile GDAX) cryptocurrency exchange. For authenticated flow, users must have valid api, secret and passphrase to be able to connect.

Maintained by Dheeraj Agarwal. Last updated 1 years ago.

coinbase-pro coinbase-pro-api coinbasepro coinbasepro-api cryptocurrency gdax gdax-r library mit-license rstudio unofficial-wrappers wrapper

21.3 match 34 stars 5.23 score 33 scripts

ironholds

WikipediR:A MediaWiki API Wrapper

A wrapper for the MediaWiki API, aimed particularly at the Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve page text, information about users or the history of pages, and elements of the category tree.

Maintained by Os Keyes. Last updated 12 months ago.

api-client api-wrapper mediawiki

11.4 match 70 stars 9.56 score 81 scripts 32 dependents

ugroempi

DoE.wrapper:Wrapper Package for Design of Experiments Functionality

Various kinds of designs for (industrial) experiments can be created. The package uses, and sometimes enhances, design generation routines from other packages. So far, response surface designs from package 'rsm', Latin hypercube samples from packages 'lhs' and 'DiceDesign', and D-optimal designs from package 'AlgDesign' have been implemented.

Maintained by Ulrike Groemping. Last updated 2 years ago.

42.3 match 2.45 score 27 scripts 2 dependents

thevaachandereng

bayesCT:Simulation and Analysis of Adaptive Bayesian Clinical Trials

Simulation and analysis of Bayesian adaptive clinical trials for binomial, continuous, and time-to-event data types, incorporates historical data and allows early stopping for futility or early success. The package uses novel and efficient Monte Carlo methods for estimating Bayesian posterior probabilities, evaluation of loss to follow up, and imputation of incomplete data. The package has the functionality for dynamically incorporating historical data into the analysis via the power prior or non-informative priors.

Maintained by Thevaa Chandereng. Last updated 5 years ago.

adaptive bayesian-methods bayesian-trial clinical-trials statistical-power

16.1 match 14 stars 6.30 score 36 scripts

dynverse

dynwrap:Representing and Inferring Single-Cell Trajectories

Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

trajectory-inference

13.2 match 16 stars 7.48 score 159 scripts 1 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.

7.3 match 845 stars 13.57 score 264 scripts 2 dependents

igdawg

BIGDAWG:Case-Cotrol Analysis of Multi-Allelic Loci

Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.

Maintained by Steve Mack. Last updated 2 years ago.

16.0 match 3 stars 6.10 score 4 scripts 2 dependents

tagteam

riskRegression:Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.

Maintained by Thomas Alexander Gerds. Last updated 17 days ago.

openblas cpp

7.4 match 46 stars 13.00 score 736 scripts 35 dependents

uscbiostats

slurmR:A Lightweight Wrapper for 'Slurm'

'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package.

Maintained by George Vega Yon. Last updated 1 years ago.

bioinformatics hpc slurm

11.5 match 59 stars 8.06 score 216 scripts 1 dependents

cran

Platypus:Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Maintained by Alexander Yermanos. Last updated 5 months ago.

20.0 match 4.58 score 38 scripts

oganm

homologene:Quick Access to Homologene and Gene Annotation Updates

A wrapper for the homologene database by the National Center for Biotechnology Information ('NCBI'). It allows searching for gene homologs across species. Data in this package can be found at <ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build68/>. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.

Maintained by Ogan Mancarci. Last updated 1 years ago.

bioinformatics homologene mancarci-2017 ncbi-taxonomy ogan-bio species wrapper

11.5 match 42 stars 7.87 score 164 scripts 4 dependents

predictiveecology

SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 18 days ago.

discrete-events-simulations simulation-framework simulation-modeling

8.5 match 10 stars 10.61 score 142 scripts 6 dependents

enblacar

SCpubr:Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

Maintained by Enrique Blanco-Carmona. Last updated 1 months ago.

software singlecell visualization data-visualization ggplot2 publication-quality-plots seurat single-cell single-cell-genomics single-cell-rna-seq

10.3 match 178 stars 8.71 score 194 scripts

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

7.9 match 137 stars 11.11 score 390 scripts 12 dependents

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 23 days ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

8.5 match 181 stars 10.16 score 252 scripts

ropensci

rredlist:'IUCN' Red List Client

'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

Maintained by William Gearty. Last updated 1 months ago.

iucn biodiversity api web-services traits habitat species conservation api-wrapper iucn-red-list taxize

7.5 match 53 stars 11.49 score 195 scripts 24 dependents

usdaforestservice

FIESTA:Forest Inventory Estimation and Analysis

A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.

Maintained by Grayson White. Last updated 2 days ago.

11.6 match 30 stars 7.24 score 62 scripts

miraisolutions

XLConnect:Excel Connector for R

Provides comprehensive functionality to read, write and format Excel data.

Maintained by Martin Studer. Last updated 17 days ago.

cross-platform excel r-language xlconnect openjdk

6.9 match 130 stars 12.28 score 1.2k scripts 1 dependents

ropengov

giscoR:Download Map Data from GISCO API - Eurostat

Tools to download data from the GISCO (Geographic Information System of the Commission) Eurostat database <https://ec.europa.eu/eurostat/web/gisco>. Global and European map data available. This package is in no way officially related to or endorsed by Eurostat.

Maintained by Diego Hernangómez. Last updated 30 days ago.

ropengov spatial api-wrapper eurostat gisco thematic-maps eurostat-data ggplot2 gis

7.5 match 75 stars 10.70 score 424 scripts 5 dependents

alexanderrobitzsch

sirt:Supplementary Item Response Theory Models

Supplementary functions for item response models aiming to complement existing R packages. The functionality includes among others multidimensional compensatory and noncompensatory IRT models (Reckase, 2009, <doi:10.1007/978-0-387-89976-3>), MCMC for hierarchical IRT models and testlet models (Fox, 2010, <doi:10.1007/978-1-4419-0742-4>), NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>), Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>; Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>), faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011, <doi:10.1111/j.1745-3984.2011.00143.x>), ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>), DETECT statistic (Stout, Habing, Douglas & Kim, 1996, <doi:10.1177/014662169602000403>), local structural equation modeling (LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016, <doi:10.1080/00273171.2016.1142856>).

Maintained by Alexander Robitzsch. Last updated 3 months ago.

item-response-theory openblas cpp

8.0 match 23 stars 10.01 score 280 scripts 22 dependents

keberwein

blscrapeR:An API Wrapper for the United States Bureau of Labor Statistics

Scrapes various data from <https://www.bls.gov/>. The Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.

Maintained by Kris Eberwein. Last updated 1 years ago.

api api-wrapper bls bureau-of-labor-statistics consumer-price-index cpi inflation inflation-calculator labor-statistics unemployment

10.4 match 112 stars 7.66 score 270 scripts

t-kalinowski

keras: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 11 months ago.

7.2 match 10.82 score 10k scripts 54 dependents

vpetukhov

ggrastr:Rasterize Layers for 'ggplot2'

Rasterize only specific layers of a 'ggplot2' plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without loosing vector properties of the scale-sensitive information.

Maintained by Evan Biederstedt. Last updated 2 years ago.

5.9 match 220 stars 13.31 score 1.9k scripts 52 dependents

ropensci

rcrossref:Client for Various 'CrossRef' 'APIs'

Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.

Maintained by Najko Jahn. Last updated 2 years ago.

text-ming literature pdf xml publications citations full-text tdm crossref api api-wrapper crossref-api doi metadata

7.5 match 172 stars 10.18 score 404 scripts 10 dependents

bioc

SingleMoleculeFootprinting:Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Maintained by Guido Barzaghi. Last updated 27 days ago.

dnamethylation coverage nucleosomepositioning datarepresentation epigenetics methylseq qualitycontrol sequencing

11.9 match 2 stars 6.43 score 27 scripts

tidyverse

stringr:Simple, Consistent Wrappers for Common String Operations

A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

Maintained by Hadley Wickham. Last updated 7 months ago.

regular-expression strings

3.4 match 622 stars 21.97 score 164k scripts 8.2k dependents

bioc

MAST:Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Maintained by Andrew McDavid. Last updated 5 months ago.

geneexpression differentialexpression genesetenrichment rnaseq transcriptomics singlecell

5.9 match 230 stars 12.75 score 1.8k scripts 5 dependents

ropensci

tradestatistics:Open Trade Statistics API Wrapper and Utility Program

Access 'Open Trade Statistics' API from R to download international trade data.

Maintained by Mauricio Vargas. Last updated 7 months ago.

api-wrapper data-table international-trade jsonlite open-trade-statistics

10.4 match 77 stars 7.15 score 92 scripts

ropensci

worrms:World Register of Marine Species (WoRMS) Client

Client for World Register of Marine Species (<https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.

Maintained by Bart Vanhoorne.. Last updated 1 years ago.

biology science marine api web api-client worms species api-wrapper biological-data fish jerico-relevant marine-biology marine-species taxize taxonomy

7.5 match 27 stars 9.79 score 372 scripts 23 dependents

kornl

mutoss:Unified Multiple Testing Procedures

Designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying 'mutossGUI'.

Maintained by Kornelius Rohmeyer. Last updated 12 months ago.

8.5 match 4 stars 8.44 score 24 scripts 16 dependents

ropensci

PostcodesioR:API Wrapper Around 'Postcodes.io'

Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.

Maintained by Eryk Walczak. Last updated 2 years ago.

api-wrapper geocoder geographic-data peer-reviewed postcode uk

11.0 match 41 stars 6.49 score 50 scripts

open-eo

openeo:Client Interface for 'openEO' Servers

Access data and processing functionalities of 'openEO' compliant back-ends in R.

Maintained by Florian Lahn. Last updated 2 months ago.

openeo openeo-user

8.3 match 64 stars 8.65 score 128 scripts

bioc

spatialDE:R wrapper for SpatialDE

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

Maintained by Gabriele Sales. Last updated 5 months ago.

software transcriptomics python spatial-data wrapper

14.9 match 3 stars 4.76 score 16 scripts

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

7.5 match 82 stars 9.27 score 191 scripts

ropensci

elastic:General Purpose Interface to 'Elasticsearch'

Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.

Maintained by Scott Chamberlain. Last updated 2 years ago.

database elasticsearch http api search nosql java json documents data-science database-wrapper etl

7.5 match 247 stars 8.98 score 151 scripts 1 dependents

yihui

animation:A Gallery of Animations in Statistics and Utilities to Create Animations

Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.

Maintained by Yihui Xie. Last updated 2 years ago.

animation statistical-computing statistical-graphics statistics

5.5 match 208 stars 12.08 score 2.5k scripts 29 dependents

svkucheryavski

mdatools:Multivariate Data Analysis for Chemometrics

Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.

Maintained by Sergey Kucheryavskiy. Last updated 8 months ago.

9.0 match 35 stars 7.37 score 220 scripts 1 dependents

robinhankin

gsl:Wrapper for the Gnu Scientific Library

An R wrapper for some of the functionality of the Gnu Scientific Library.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

gsl

5.6 match 15 stars 11.82 score 472 scripts 204 dependents

ropensci

ckanr:Client for the Comprehensive Knowledge Archive Network ('CKAN') API

Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.

Maintained by Francisco Alves. Last updated 2 years ago.

database open-data ckan api data dataset api-wrapper ckan-api

7.5 match 100 stars 8.67 score 448 scripts 4 dependents

ropensci

rvertnet:Search 'Vertnet', a 'Database' of Vertebrate Specimen Records

Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.

Maintained by Dave Slager. Last updated 5 months ago.

species occurrences biodiversity maps vertnet mammals mammalia specimens api-wrapper specimen spocc

7.5 match 7 stars 8.51 score 35 scripts 6 dependents

benkeser

nlpred:Estimators of Non-Linear Cross-Validated Risks Optimized for Small Samples

Methods for obtaining improved estimates of non-linear cross-validated risks are obtained using targeted minimum loss-based estimation, estimating equations, and one-step estimation (Benkeser, Petersen, van der Laan (2019), <doi:10.1080/01621459.2019.1668794>). Cross-validated area under the receiver operating characteristics curve (LeDell, Petersen, van der Laan (2015), <doi:10.1214/15-EJS1035>) and other metrics are included.

Maintained by David Benkeser. Last updated 3 years ago.

auc cross-validation estimating-equations machine-learning tmle

15.2 match 3 stars 4.18 score 6 scripts

kbhoehn

dowser:B Cell Receptor Phylogenetics Toolkit

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Maintained by Kenneth Hoehn. Last updated 2 months ago.

9.3 match 6.81 score 84 scripts

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 2 days ago.

openblas fftw3 cpp openmp

9.4 match 10 stars 6.68 score 476 scripts

ropensci

gistr:Work with 'GitHub' 'Gists'

Work with 'GitHub' 'gists' from 'R' (e.g., <https://en.wikipedia.org/wiki/GitHub#Gist>, <https://docs.github.com/en/github/writing-on-github/creating-gists/>). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: <https://gist.github.com/>.

Maintained by Scott Chamberlain. Last updated 2 years ago.

http https api web-services github github api gist gists code script snippet api-wrapper github-api github-gist

7.5 match 104 stars 8.30 score 42 scripts 2 dependents

edzer

sp:Classes and Methods for Spatial Data

Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.

Maintained by Edzer Pebesma. Last updated 2 months ago.

3.3 match 127 stars 18.63 score 35k scripts 1.3k dependents

predictiveecology

LandR:Landscape Ecosystem Modelling in R

Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 3 days ago.

ecological-modelling landscape-ecosystem-modelling spades

10.1 match 17 stars 6.07 score 12 scripts 4 dependents

johannesfriedrich

hystReet:Get Pedestrian Frequency Data from the 'Hystreet' Project

An R API wrapper for the 'Hystreet' project <https://hystreet.com>. 'Hystreet' provides pedestrian counts in different cities in Germany.

Maintained by Johannes Friedrich. Last updated 2 months ago.

api bigdata hystreet pedestrian-detection wrapper

11.5 match 13 stars 5.29 score 9 scripts

adrientaudiere

MiscMetabar:Miscellaneous Functions for Metabarcoding Analysis

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.

Maintained by Adrien Taudière. Last updated 25 days ago.

sequencing microbiome metagenomics clustering classification visualization amplicon amplicon-sequencing biodiversity-informatics ecology illumina metabarcoding ngs-analysis

9.4 match 17 stars 6.44 score 23 scripts

dieghernan

nominatimlite:Interface with 'Nominatim' API Service

Lite interface for getting data from 'OSM' service 'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract coordinates from addresses, find places near a set of coordinates and return spatial objects on 'sf' format.

Maintained by Diego Hernangómez. Last updated 1 months ago.

geocoding openstreetmap address nominatim reverse-geocoding shapefile spatial api-wrapper api gis

7.5 match 20 stars 8.08 score 41 scripts 1 dependents

boxiang-wang

ARTtransfer:Adaptive and Robust Pipeline for Transfer Learning

Adaptive and Robust Transfer Learning (ART) is a flexible framework for transfer learning that integrates information from auxiliary data sources to improve model performance on primary tasks. It is designed to be robust against negative transfer by including the non-transfer model in the candidate pool, ensuring stable performance even when auxiliary datasets are less informative. See the paper, Wang, Wu, and Ye (2023) <doi:10.1002/sta4.582>.

Maintained by Boxiang Wang. Last updated 2 months ago.

13.7 match 4.40 score 1 scripts

rstudio

DT:A Wrapper of the JavaScript Library 'DataTables'

Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.

Maintained by Joe Cheng. Last updated 3 months ago.

datatables htmlwidgets javascript shiny

3.1 match 604 stars 19.15 score 38k scripts 673 dependents

dipterix

dipsaus:A Dipping Sauce for Data Analysis and Visualizations

Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.

Maintained by Zhengjia Wang. Last updated 5 days ago.

cpp

7.6 match 13 stars 7.90 score 85 scripts 3 dependents

muschellij2

freesurfer:Wrapper Functions for 'Freesurfer'

Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.

Maintained by John Muschelli. Last updated 3 months ago.

7.7 match 10 stars 7.69 score 55 scripts 1 dependents

amices

mice:Multivariate Imputation by Chained Equations

Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

Maintained by Stef van Buuren. Last updated 6 days ago.

chained-equations fcs imputation mice missing-data missing-values multiple-imputation multivariate-data cpp

3.6 match 462 stars 16.50 score 10k scripts 154 dependents

ropensci

fingertipsR:Fingertips Data for Public Health

Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.

Maintained by Annabel Westermann. Last updated 1 years ago.

api-wrapper fingertips health open-data peer-reviewed public-health public-health-england

7.5 match 96 stars 7.89 score 268 scripts 1 dependents

bioc

CellBench:Construct Benchmarks for Single Cell Analysis Methods

This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

Maintained by Shian Su. Last updated 5 months ago.

software infrastructure singlecell benchmark bioinformatics

6.8 match 30 stars 8.71 score 98 scripts

quanteda

spacyr:Wrapper to the 'spaCy' 'NLP' Library

An R wrapper to the 'Python' 'spaCy' 'NLP' library, from <https://spacy.io>.

Maintained by Kenneth Benoit. Last updated 1 months ago.

extract-entities nlp spacy speech-tagging

5.5 match 253 stars 10.68 score 408 scripts 6 dependents

bioc

CNEr:CNE Detection and Visualization

Large-scale identification and advanced visualization of sets of conserved noncoding elements.

Maintained by Ge Tan. Last updated 5 months ago.

generegulation visualization dataimport

6.3 match 3 stars 9.28 score 35 scripts 19 dependents

cschwarz-stat-sfu-ca

BTSPAS:Bayesian Time-Stratified Population Analysis

Provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. Theory described in Bonner and Schwarz (2011) <doi:10.1111/j.1541-0420.2011.01599.x>.

Maintained by Carl J Schwarz. Last updated 5 months ago.

jags cpp

9.7 match 1 stars 6.04 score 28 scripts 1 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 1 months ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper itis taxize

7.5 match 16 stars 7.72 score 64 scripts 24 dependents

predictiveecology

reproducible:Enhance Reproducibility of R Code

A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().

Maintained by Eliot J B McIntire. Last updated 30 days ago.

reproducibility reproducible-research

5.5 match 41 stars 10.52 score 122 scripts 15 dependents

wikimedia

WikidataQueryServiceR:API Client Library for 'Wikidata Query Service'

An API client for the 'Wikidata Query Service' <https://query.wikidata.org/>.

Maintained by Mikhail Popov. Last updated 5 years ago.

api-wrapper sparql wdqs wikidata

7.5 match 28 stars 7.67 score 73 scripts 31 dependents

jdthorpe

ajv:Another JSON Schema Validator

A thin wrapper around the 'ajv' JSON validation package for JavaScript. See <http://epoberezkin.github.io/ajv/> for details.

Maintained by Jason Thorpe. Last updated 8 years ago.

15.5 match 3.70 score 8 scripts

abhi-1u

texor:Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'

Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.

Maintained by Abhishek Ulayil. Last updated 3 months ago.

9.1 match 7 stars 6.28 score 8 scripts

clement-lee

crandep:Network Analysis of Dependencies of CRAN Packages

The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.

Maintained by Clement Lee. Last updated 7 months ago.

openblas cpp

9.0 match 8 stars 6.23 score 20 scripts

r-spatial

link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.

Maintained by Chris Reudenbach. Last updated 4 months ago.

6.1 match 26 stars 9.05 score 78 scripts 1 dependents

pcruniversum

RDML:Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.

Maintained by Konstantin A. Blagodatskikh. Last updated 7 months ago.

bioinformatics pcr qpcr rdml

7.5 match 21 stars 7.16 score 58 scripts 1 dependents

kapelner

fastLogisticRegressionWrap:Fast Logistic Regression Wrapper

Provides very fast logistic regression with coefficient inferences plus other useful methods such as a forward stepwise model generator (see the benchmarks by visiting the github page at the URL below). The inputs are flexible enough to accomodate GPU computations. The coefficient estimation employs the fastLR() method in the 'RcppNumerical' package by Yixuan Qiu et al. This package allows their work to be more useful to a wider community that consumes inference.

Maintained by Adam Kapelner. Last updated 23 days ago.

cpp

19.6 match 1 stars 2.70 score 2 scripts

rladies

meetupr:Meetup R API

Provides access to data from <https:www.meetup.com> (see <https:www.meetup.com/meetup_api/> for more information).

Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.

api api-wrapper meetup r-ladies rladies rladies-global

7.5 match 77 stars 7.03 score 92 scripts

stevenmmortimer

rdfp:An Implementation of the 'DoubleClick for Publishers' API

Functions to interact with the 'Google DoubleClick for Publishers (DFP)' API <https://developers.google.com/ad-manager/api/start> (recently renamed to 'Google Ad Manager'). This package is automatically compiled from the API WSDL (Web Service Description Language) files to dictate how the API is structured. Theoretically, all API actions are possible using this package; however, care must be taken to format the inputs correctly and parse the outputs correctly. Please see the 'Google Ad Manager' API reference <https://developers.google.com/ad-manager/api/rel_notes> and this package's website <https://stevenmmortimer.github.io/rdfp/> for more information, documentation, and examples.

Maintained by Steven M. Mortimer. Last updated 6 years ago.

api-client api-wrapper dfp dfp-api doubleclick doubleclick-for-publishers google-dfp

7.5 match 16 stars 6.93 score 214 scripts

stocnet

ERPM:Exponential Random Partition Models

Simulates and estimates the Exponential Random Partition Model presented in the paper Hoffman, Block, and Snijders (2023) <doi:10.1177/00811750221145166>. It can also be used to estimate longitudinal partitions, following the model proposed in Hoffman and Chabot (2023) <doi:10.1016/j.socnet.2023.04.002>. The model is an exponential family distribution on the space of partitions (sets of non-overlapping groups) and is called in reference to the Exponential Random Graph Models (ERGM) for networks.

Maintained by Marion Hoffman. Last updated 10 months ago.

10.8 match 10 stars 4.78 score

bioc

MBECS:Evaluation and correction of batch effects in microbiome data-sets

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

Maintained by Michael Olbrich. Last updated 5 months ago.

batcheffect microbiome reportwriting visualization normalization qualitycontrol

11.2 match 4 stars 4.60 score 4 scripts

tguillerme

dispRity:Measuring Disparity

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

Maintained by Thomas Guillerme. Last updated 2 days ago.

disparity ecology multidimensionality palaeobiology

5.9 match 26 stars 8.69 score 220 scripts 1 dependents

egeulgen

pathfindR:Enrichment Analysis Utilizing Active Subnetworks

Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Maintained by Ege Ulgen. Last updated 27 days ago.

active-subnetworks enrichment pathway pathway-enrichment-analysis subnetwork

5.0 match 186 stars 10.13 score 138 scripts

aschleg

PetfindeR:'Petfinder' API Wrapper

Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.

Maintained by Aaron Schlegel. Last updated 5 years ago.

animal-shelter animal-welfare-organizations animals api-wrapper petfinder petfinder-api petfinder-database

11.3 match 6 stars 4.48 score 6 scripts

wraysmith

caRecall:Government of Canada Vehicle Recalls Database API Wrapper

Provides API access to the Government of Canada Vehicle Recalls Database <https://tc.api.canada.ca/en/detail?api=VRDB> used by the Defect Investigations and Recalls Division for vehicles, tires, and child car seats. The API wrapper provides access to recall summary information searched using make, model, and year range, as well as detailed recall information searched using recall number.

Maintained by Nathan Smith. Last updated 4 years ago.

api-wrapper vehicle-recalls-database

10.9 match 4 stars 4.60 score 2 scripts

t-grimes

dnapath:Differential Network Analysis using Gene Pathways

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.

Maintained by Tyler Grimes. Last updated 22 days ago.

cpp

21.5 match 2.30 score 5 scripts

ropensci

cyphr:High Level Encryption Wrappers

Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.

Maintained by Rich FitzJohn. Last updated 1 months ago.

encryption openssl peer-reviewed sodium

5.8 match 94 stars 8.51 score 36 scripts 2 dependents

radiant-rstats

radiant.data:Data Menu for Radiant: Business Analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

Maintained by Vincent Nijs. Last updated 5 months ago.

5.8 match 54 stars 8.30 score 146 scripts 6 dependents

rconsortium

S7:An Object Oriented System Meant to Become a Successor to S3 and S4

A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.

Maintained by Hadley Wickham. Last updated 4 months ago.

3.7 match 432 stars 13.15 score 86 scripts 22 dependents

mathsinhealth

eq5dsuite:Manipulating and Analysing EQ-5d Data

The EQ-5D is a widely-used standarized instrument for measuring Health Related Quality Of Life (HRQOL), developed by the EuroQol group <https://euroqol.org/>. It assesses five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression, using either a three-level (EQ-5D-3L) or five-level (EQ-5D-5L) scale. Scores from these dimensions are commonly converted into a single utility index using country-specific value sets, which are critical in clinical and economic evaluations of healthcare and in population health surveys. The eq5dsuite package enables users to calculate utility index values for the EQ-5D instruments, including crosswalk utilities using the original crosswalk developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008> (mapping EQ-5D-5L responses to EQ-5D-3L index values), or the recently developed reverse crosswalk by van Hout et al. (2021) <doi:10.1016/j.jval.2021.03.009> (mapping EQ-5D-3L responses to EQ-5D-5L index values). Users are allowed to add and/or remove user-defined value sets. Additionally, the package provides tools to analyze EQ-5D data according to the recommended guidelines outlined in "Methods for Analyzing and Reporting EQ-5D data" by Devlin et al. (2020) <doi:10.1007/978-3-030-47622-9>.

Maintained by Kim Rand. Last updated 10 months ago.

12.2 match 3.95 score 1 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 1 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

5.1 match 44 stars 9.45 score 472 scripts

rmgpanw

gtexr:Query the GTEx Portal API

A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. For more information on the API, see <https://gtexportal.org/api/v2/redoc>.

Maintained by Alasdair Warwick. Last updated 6 months ago.

api-wrapper bioinformatics eqtl gtex sqtl

7.5 match 5 stars 6.41 score 5 scripts

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

3.9 match 261 stars 12.39 score 406 scripts 14 dependents

modeloriented

DALEXtra:Extension for 'DALEX' Package

Provides wrapper of various machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the interpretable machine learning, there are more and more new ideas for explaining black-box models, that are implemented in 'R'. 'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library. Important part of the package is Champion-Challenger analysis and innovative approach to model performance across subsets of test data presented in Funnel Plot.

Maintained by Szymon Maksymiuk. Last updated 2 years ago.

extension-for-dalex-package

6.2 match 67 stars 7.71 score 400 scripts 1 dependents

rywhale

kiwisR:A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS' API

A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides access to 'WISKI' databases via HTTP requests (<https://www.kisters.eu/water-weather-and-environment/>). Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL. Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.

Maintained by Ryan Whaley. Last updated 5 months ago.

api-wrapper hydrology hydrometrics kisters open-data r-programming

12.5 match 13 stars 3.81 score 10 scripts

tidymodels

bonsai:Model Wrappers for Tree-Based Models

Bindings for additional tree-based model engines for use with the 'parsnip' package. Models include gradient boosted decision trees with 'LightGBM' (Ke et al, 2017.), conditional inference trees and conditional random forests with 'partykit' (Hothorn and Zeileis, 2015. and Hothorn et al, 2006. <doi:10.1198/106186006X133933>), and accelerated oblique random forests with 'aorsf' (Jaeger et al, 2022 <doi:10.5281/zenodo.7116854>).

Maintained by Simon Couch. Last updated 1 months ago.

4.8 match 52 stars 9.97 score 620 scripts 2 dependents

shusei-e

RcppJagger:An R Wrapper for Jagger

A wrapper for Jagger, a morphological analyzer proposed in Yoshinaga (2023) <arXiv:2305.19045>. Jagger uses patterns derived from morphological dictionaries and training data sets and applies them from the beginning of the input. This simultaneous and deterministic process enables it to effectively perform tokenization, POS tagging, and lemmatization.

Maintained by Shusei Eshima. Last updated 2 years ago.

japanese-nlp morphological-analyser nlp part-of-speech-tagger text-analysis cpp

14.6 match 3 stars 3.18 score 3 scripts

snoweye

pbdZMQ:Programming with Big Data -- Interface to 'ZeroMQ'

'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.

Maintained by Wei-Chen Chen. Last updated 6 months ago.

zeromq3

4.7 match 17 stars 9.92 score 46 scripts 26 dependents

bioc

igvShiny:igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

Maintained by Arkadiusz Gladki. Last updated 5 months ago.

software shinyapps sequencing coverage

6.2 match 37 stars 7.40 score 120 scripts

thomaswiemann

ddml:Double/Debiased Machine Learning

Estimate common causal parameters using double/debiased machine learning as proposed by Chernozhukov et al. (2018) <doi:10.1111/ectj.12097>. 'ddml' simplifies estimation based on (short-)stacking as discussed in Ahrens et al. (2024) <doi:10.1177/1536867X241233641>, which leverages multiple base learners to increase robustness to the underlying data generating process.

Maintained by Thomas Wiemann. Last updated 4 months ago.

7.5 match 17 stars 6.12 score 31 scripts

aschleg

Rpoet:'PoetryDB' API Wrapper

Wrapper for the 'PoetryDB' API <http://poetrydb.org> that allows for interaction and data extraction from the database in an R interface. The 'PoetryDB' API is a database of poetry and poets implemented with 'MongoDB' to enable developers and poets to easily access one of the most comprehensive poetry databases currently available.

Maintained by Aaron Schlegel. Last updated 6 years ago.

api-wrapper poetry

11.3 match 2 stars 4.00 score 3 scripts

randrescastaneda

joyn:Tool for Diagnosis of Tables Joins and Complementary Join Features

Tool for diagnosing table joins. It combines the speed of `collapse` and `data.table`, the flexibility of `dplyr`, and the diagnosis and features of the `merge` command in `Stata`.

Maintained by R.Andres Castaneda. Last updated 3 months ago.

join merge

6.5 match 9 stars 7.00 score 31 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

5.9 match 40 stars 7.69 score 144 scripts

bioc

decoupleR:decoupleR: Ensemble of computational methods to infer biological activities from omics data

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

Maintained by Pau Badia-i-Mompel. Last updated 5 months ago.

differentialexpression functionalgenomics geneexpression generegulation network software statisticalmethod transcription

4.0 match 230 stars 11.27 score 316 scripts 3 dependents

j-mitchel

scITD:Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Maintained by Jonathan Mitchel. Last updated 2 years ago.

cpp

22.7 match 1.98 score 19 scripts

zumbov2

deeplr:Interface to the 'DeepL' Translation API

A wrapper for the 'DeepL' Pro API <https://www.deepl.com/docs-api>, a web service for translating texts between different languages. A DeepL API developer account is required to use the service (see <https://www.deepl.com/pro#developer>).

Maintained by David Zumbach. Last updated 12 months ago.

api-wrapper deepl translation

8.0 match 41 stars 5.57 score 70 scripts

mimno

mallet:An R Wrapper for the Java Mallet Topic Modeling Toolkit

An R interface for the Java Machine Learning for Language Toolkit (mallet) <https://mimno.github.io/Mallet/> to estimate probabilistic topic models, such as Latent Dirichlet Allocation. We can use the R package to read textual data into 'mallet' from R objects, run the Java implementation of 'mallet' directly in R, and extract results as R objects. The 'mallet' toolkit has many functions, this wrapper focuses on the topic modeling sub-package written by David Mimno. The package uses the 'rJava' package to connect to a Java Virtual Machine (JVM).

Maintained by Måns Magnusson. Last updated 3 years ago.

openjdk

5.1 match 38 stars 8.62 score 141 scripts 3 dependents

moosa-r

rbioapi:User-Friendly R Interface to Biologic Web Services' API

Currently fully supports Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt! The goal of rbioapi is to provide a user-friendly and consistent interface to biological databases and services. In a way that insulates the user from the technicalities of using web services API and creates a unified and easy-to-use interface to biological and medical web services. This is an ongoing project; New databases and services will be added periodically. Feel free to suggest any databases or services you often use.

Maintained by Moosa Rezwani. Last updated 1 months ago.

api-client bioinformatics biology enrichment enrichment-analysis enrichr jaspar mieaa over-representation-analysis panther reactome string uniprot

5.7 match 20 stars 7.60 score 55 scripts

globalfishingwatch

gfwr:Access data from Global Fishing Watch APIs

This package connects to several Global Fishing Watch APIs to get vessel and events information in an R-friendly format.

Maintained by Andrea Sánchez-Tapia. Last updated 2 months ago.

api-wrapper globalfishingwatch mapping

7.5 match 63 stars 5.79 score 66 scripts

bioc

Rbwa:R wrapper for BWA-backtrack and BWA-MEM aligners

Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

Maintained by Jean-Philippe Fortin. Last updated 5 months ago.

sequencing alignment bwa bwa-mem dna-sequences dna-sequencing

10.2 match 1 stars 4.26 score 10 scripts 1 dependents

ropensci

npi:Access the U.S. National Provider Identifier Registry API

Access the United States National Provider Identifier Registry API <https://npiregistry.cms.hhs.gov/api/>. Obtain and transform administrative data linked to a specific individual or organizational healthcare provider, or perform advanced searches based on provider name, location, type of service, credentials, and other attributes exposed by the API.

Maintained by Frank Farach. Last updated 1 months ago.

api-wrapper health-data healthcare npi-number

7.5 match 36 stars 5.76 score 16 scripts

bstewart

stm:Estimation of the Structural Topic Model

The Structural Topic Model (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions. Methods developed in Roberts et. al. (2014) <doi:10.1111/ajps.12103> and Roberts et. al. (2016) <doi:10.1080/01621459.2016.1141684>. Vignette is Roberts et. al. (2019) <doi:10.18637/jss.v091.i02>.

Maintained by Brandon Stewart. Last updated 1 years ago.

openblas cpp

3.4 match 404 stars 12.63 score 1.6k scripts 6 dependents

edwinth

padr:Quickly Get Datetime Data Ready for Analysis

Transforms datetime data into a format ready for analysis. It offers two core functionalities; aggregating data to a higher level interval (thicken) and imputing records where observations were absent (pad).

Maintained by Edwin Thoen. Last updated 4 months ago.

cpp

3.8 match 132 stars 11.49 score 428 scripts 20 dependents

ropensci

bold:Interface to Bold Systems API

A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.

Maintained by Salix Dubois. Last updated 3 months ago.

biodiversity barcode dna sequences fasta api-wrapper barcodes taxize

7.5 match 18 stars 5.74 score 57 scripts

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.

5.9 match 8 stars 7.33 score 12 scripts 78 dependents

epiforecasts

EpiSoon:Forecast Cases Using Reproduction Numbers

To forecast the time-varying reproduction number and use this to forecast reported case counts. Includes tools to evaluate a range of models across samples and time series using proper scoring rules.

Maintained by Sam Abbott. Last updated 2 years ago.

case-forecasts forecasts

10.0 match 7 stars 4.26 score 25 scripts 1 dependents

mrcieu

ieugwasr:Interface to the 'OpenGWAS' Database API

Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Maintained by Gibran Hemani. Last updated 2 days ago.

4.0 match 89 stars 10.71 score 404 scripts 6 dependents

bioc

uSORT:uSORT: A self-refining ordering pipeline for gene selection

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.

Maintained by Hao Chen. Last updated 5 months ago.

immunooncology rnaseq gui cellbiology dnaseq

12.8 match 3.30 score

till-tietz

parsel:Parallel Dynamic Web-Scraping Using 'RSelenium'

A system to increase the efficiency of dynamic web-scraping with 'RSelenium' by leveraging parallel processing. You provide a function wrapper for your 'RSelenium' scraping routine with a set of inputs, and 'parsel' runs it in several browser instances. Chunked input processing as well as error catching and logging ensures seamless execution and minimal data loss, even when unforeseen 'RSelenium' errors occur. You can additionally build safe scraping functions with minimal coding by utilizing constructor functions that act as wrappers around 'RSelenium' methods.

Maintained by Till Tietz. Last updated 1 years ago.

parallel rselenium web-scraping

10.8 match 15 stars 3.88 score 8 scripts

dieghernan

arcgeocoder:Geocoding with the 'ArcGIS' REST API Service

Lite interface for finding locations of addresses or businesses around the world using the 'ArcGIS' REST API service <https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>. Address text can be converted to location candidates and a location can be converted into an address. No API key required.

Maintained by Diego Hernangómez. Last updated 1 months ago.

geocoding arcgis address reverse-geocoding api-wrapper api-rest arcgis-api gis

7.5 match 2 stars 5.56 score 15 scripts

fkoh111

zzlite:Lite Wrapper for the 'Zamzar File Conversion' API

A minor collection of HTTP wrappers for the 'Zamzar File Conversion' API. The wrappers makes it easy to utilize the API and thus convert between more than 100 different file formats (ranging from audio files, images, movie formats, etc., etc.) through an R session. For specifics regarding the API, please see <https://developers.zamzar.com/>.

Maintained by Frederik Kok Hansen. Last updated 5 years ago.

api api-wrapper conversion zamzar-api

11.2 match 3.70 score 1 scripts

lme4

lme4:Linear Mixed-Effects Models using 'Eigen' and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Maintained by Ben Bolker. Last updated 2 days ago.

cpp

2.0 match 647 stars 20.69 score 35k scripts 1.5k dependents

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 2 days ago.

microbiome software dataimport analysis bioconductor

3.6 match 52 stars 11.50 score 316 scripts 5 dependents

bioc

metagenomeSeq:Statistical analysis for sparse high-throughput sequencing

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

Maintained by Joseph N. Paulson. Last updated 3 months ago.

immunooncology classification clustering geneticvariability differentialexpression microbiome metagenomics normalization visualization multiplecomparison sequencing software

3.4 match 69 stars 12.02 score 494 scripts 7 dependents

jeanimal

heuristica:Heuristics Including Take the Best and Unit-Weight Linear

Implements various heuristics like Take The Best and unit-weight linear, which do two-alternative choice: which of two objects will have a higher criterion? Also offers functions to assess performance, e.g. percent correct across all row pairs in a data set and finding row pairs where models disagree. New models can be added by implementing a fit and predict function-- see vignette. Take The Best was first described in: Gigerenzer, G. & Goldstein, D. G. (1996) <doi:10.1037/0033-295X.103.4.650>. All of these heuristics were run on many data sets and analyzed in: Gigerenzer, G., Todd, P. M., & the ABC Group (1999). <ISBN:978-0195143812>.

Maintained by Jean Whitmore. Last updated 1 years ago.

7.1 match 5 stars 5.75 score 45 scripts

joshobrien

gdalUtilities:Wrappers for 'GDAL' Utilities Executables

R's 'sf' package ships with self-contained 'GDAL' executables, including a bare bones interface to several 'GDAL'-related utility programs collectively known as the 'GDAL utilities'. For each of those utilities, this package provides an R wrapper whose formal arguments closely mirror those of the 'GDAL' command line interface. The utilities operate on data stored in files and typically write their output to other files. Therefore, to process data stored in any of R's more common spatial formats (i.e. those supported by the 'sf' and 'terra' packages), first write them to disk, then process them with the package's wrapper functions before reading the outputted results back into R. GDAL function arguments introduced in GDAL version 3.5.2 or earlier are supported.

Maintained by Joshua OBrien. Last updated 2 years ago.

5.8 match 37 stars 7.09 score 252 scripts 6 dependents

lorenzbr

cryptowatchR:An API Wrapper for 'Cryptowatch'

An API wrapper for 'Cryptowatch' to get prices and other information (e.g., volume, trades, order books, bid and ask prices, live quotes, and more) about cryptocurrencies and crypto exchanges. See <https://docs.cryptowat.ch/rest-api> for a detailed documentation.

Maintained by Lorenz Brachtendorf. Last updated 3 years ago.

api-wrapper cryptocurrencies cryptowatch

11.4 match 8 stars 3.60 score 7 scripts

bioc

alabaster.files:Wrappers to Save Common File Formats

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Maintained by Aaron Lun. Last updated 5 months ago.

datarepresentation dataimport

8.9 match 4.50 score 21 scripts

bioc

Rbowtie:R bowtie wrapper

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Maintained by Michael Stadler. Last updated 2 months ago.

sequencing alignment

5.8 match 1 stars 6.80 score 22 scripts 8 dependents

statnet

statnet.common:Common R Scripts and Utilities Used by the Statnet Project Software

Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.

Maintained by Pavel N. Krivitsky. Last updated 26 days ago.

3.4 match 8 stars 11.42 score 197 scripts 148 dependents

niehs

amadeus:Accessing and Analyzing Large-Scale Environmental Data

Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.

Maintained by Kyle Messier. Last updated 19 days ago.

5.5 match 8 stars 7.16 score 13 scripts

fbrun-acta

ZeBook:Working with Dynamic Models for Agriculture and Environment

R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.

Maintained by Francois Brun. Last updated 6 years ago.

16.4 match 4 stars 2.37 score 59 scripts

btskinner

rscorecard:A Method to Download Department of Education College Scorecard Data

A method to download Department of Education College Scorecard data using the public API <https://collegescorecard.ed.gov/data/data-documentation/>. It is based on the 'dplyr' model of piped commands to select and filter data in a single chained function call. An API key from the U.S. Department of Education is required.

Maintained by Benjamin Skinner. Last updated 5 months ago.

api-wrapper education-college-scorecard higher-education-data scorecard-data

7.5 match 26 stars 5.18 score 38 scripts

marcellgranat

currr:Apply Mapping Functions in Frequent Saving

Implementations of the family of map() functions with frequent saving of the intermediate results. The contained functions let you start the evaluation of the iterations where you stopped (reading the already evaluated ones from cache), and work with the currently evaluated iterations while remaining ones are running in a background job. Parallel computing is also easier with the workers parameter.

Maintained by Marcell Granat. Last updated 7 months ago.

checkpoints parallel-computing purrr

9.6 match 21 stars 4.02 score 7 scripts

bioc

metaMS:MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

Maintained by Yann Guitton. Last updated 5 months ago.

immunooncology massspectrometry metabolomics

5.2 match 15 stars 7.50 score 15 scripts

jokergoo

GetoptLong:Parsing Command-Line Arguments and Simple Variable Interpolation

This is a command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptations for easier use in R. It also provides a simple way for variable interpolation in R.

Maintained by Zuguang Gu. Last updated 2 years ago.

3.5 match 17 stars 10.98 score 478 scripts 155 dependents

chris-dworschak

disastr.api:Wrapper for the UN OCHA ReliefWeb Disaster Events API

Access and manage the application programming interface (API) of the United Nations Office for the Coordination of Humanitarian Affairs' (OCHA) ReliefWeb disaster events at <https://reliefweb.int/disasters>. The package requires a minimal number of dependencies. It offers functionality to retrieve a user-defined sample of disaster events from ReliefWeb, providing an easy alternative to scraping the ReliefWeb website. It enables a seamless integration of regular data updates into the research work flow.

Maintained by Christoph Dworschak. Last updated 11 months ago.

api-wrapper disaster-events ocha reliefweb

12.1 match 3 stars 3.18 score 6 scripts

nathaneastwood

gghalfnorm:Create a Half Normal Plot Using 'ggplot2'

Reproduce the halfnorm() function found in the 'faraway' package using the 'ggplot2' API.

Maintained by Nathan Eastwood. Last updated 8 years ago.

faraway ggplot2-api wrapper

11.0 match 2 stars 3.48 score 8 scripts 1 dependents

hafen

trelliscopejs:Create Interactive Trelliscope Displays

Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'tidyverse' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.

Maintained by Ryan Hafen. Last updated 1 years ago.

visualization

4.0 match 264 stars 9.50 score 1000 scripts 1 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

3.5 match 54 stars 11.01 score 270 scripts 4 dependents

kss2k

modsem:Latent Interaction (and Moderation) Analysis in Structural Equation Models (SEM)

Estimation of interaction (i.e., moderation) effects between latent variables in structural equation models (SEM). The supported methods are: The constrained approach (Algina & Moulder, 2001). The unconstrained approach (Marsh et al., 2004). The residual centering approach (Little et al., 2006). The double centering approach (Lin et al., 2010). The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000). The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable) The constrained- unconstrained, residual- and double centering- approaches are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches are estimated via 'modsem' it self. Alternatively model can be estimated via 'Mplus' (Muthén & Muthén, 1998-2017). References: Algina, J., & Moulder, B. C. (2001). <doi:10.1207/S15328007SEM0801_3>. "A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3." Klein, A., & Moosbrugger, H. (2000). <doi:10.1007/BF02296338>. "Maximum likelihood estimation of latent interaction effects with the LMS method." Klein, A. G., & Muthén, B. O. (2007). <doi:10.1080/00273170701710205>. "Quasi-maximum likelihood estimation of structural equation models with multiple interaction and quadratic effects." Lin, G. C., Wen, Z., Marsh, H. W., & Lin, H. S. (2010). <doi:10.1080/10705511.2010.488999>. "Structural equation models of latent interactions: Clarification of orthogonalizing and double-mean-centering strategies." Little, T. D., Bovaird, J. A., & Widaman, K. F. (2006). <doi:10.1207/s15328007sem1304_1>. "On the merits of orthogonalizing powered and product terms: Implications for modeling interactions among latent variables." Marsh, H. W., Wen, Z., & Hau, K. T. (2004). <doi:10.1037/1082-989X.9.3.275>. "Structural equation models of latent interactions: evaluation of alternative estimation strategies and indicator construction." Muthén, L.K. and Muthén, B.O. (1998-2017). "'Mplus' User’s Guide. Eighth Edition." <https://www.statmodel.com/>. Rosseel Y (2012). <doi:10.18637/jss.v048.i02>. "'lavaan': An R Package for Structural Equation Modeling."

Maintained by Kjell Solem Slupphaug. Last updated 9 days ago.

interaction-effect interaction-effects latent-moderated-structural-equations lavaan-syntax lms moderation qml quasi-maximum-likelihood rlang rlanguage sem structural-equation-modeling structural-equation-models openblas cpp openmp

4.5 match 6 stars 8.42 score 54 scripts

business-science

tibbletime:Time Aware Tibbles

Built on top of the 'tibble' package, 'tibbletime' is an extension that allows for the creation of time aware tibbles. Some immediate advantages of this include: the ability to perform time-based subsetting on tibbles, quickly summarising and aggregating results by time periods, and creating columns that can be used as 'dplyr' time-based groups.

Maintained by Davis Vaughan. Last updated 3 months ago.

periodicity tibble time time-series timeseries cpp

3.6 match 177 stars 10.51 score 644 scripts 2 dependents

ropensci

rdatacite:Client for the 'DataCite' API

Client for the web service methods provided by 'DataCite' (<https://www.datacite.org/>), including functions to interface with their 'RESTful' search API. The API is backed by 'Elasticsearch', allowing expressive queries, including faceting.

Maintained by Bianca Kramer. Last updated 2 years ago.

data scholarly dataset https api web-services api-wrapper datacite identifier metadata oai-pmh solr

7.5 match 25 stars 4.99 score 26 scripts

rstudio

reticulate:Interface to 'Python'

Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.

Maintained by Tomasz Kalinowski. Last updated 1 days ago.

cpp

1.8 match 1.7k stars 21.07 score 18k scripts 427 dependents

ecortesgomez

DiscreteGapStatistic:An Extension of the Gap Statistic for Ordinal/Categorical Data

The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.

Maintained by Eduardo Cortes. Last updated 10 days ago.

9.6 match 3.81 score 4 scripts

american-soccer-analysis

itscalledsoccer:American Soccer Analysis API Client

Provides a wrapper around the same API <https://app.americansocceranalysis.com/api/v1/__docs__/> that powers the American Soccer Analysis app.

Maintained by Tyler Richardett. Last updated 1 months ago.

api-wrapper itscalledsoccer soccer soccer-api

8.0 match 6 stars 4.56 score 3 scripts

bioc

infinityFlow:Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

Pipeline to analyze and merge data files produced by BioLegend's LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).

Maintained by Etienne Becht. Last updated 5 months ago.

software flowcytometry cellbasedassays singlecell proteomics

10.1 match 3.60 score 4 scripts

haozhu233

kableExtra:Construct Complex Table with 'kable' and Pipe Syntax

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

Maintained by Hao Zhu. Last updated 10 days ago.

html kable kableextra knitr latex rmarkdown

1.9 match 702 stars 19.35 score 55k scripts 163 dependents

arrismo

lubrilog:Get Insights on 'lubridate' Operations

Provides a set of tools designed to enhance transparency and understanding of date-time manipulation functions from the 'lubridate' package. It provides detailed feedback about the operations performed by 'lubridate' functions, allowing users to better comprehend and debug their code. These insights serve as both a learning tool for newcomers and a debugging aid for programmers working with date-time data.

Maintained by Mikael Moise. Last updated 4 months ago.

10.0 match 2 stars 3.60 score 9 scripts

rvlenth

emmeans:Estimated Marginal Means, aka Least-Squares Means

Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.

Maintained by Russell V. Lenth. Last updated 3 days ago.

1.9 match 377 stars 19.19 score 13k scripts 187 dependents

laresbernardo

lares:Analytics & Machine Learning Sidekick

Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.

Maintained by Bernardo Lares. Last updated 23 days ago.

analytics api automation automl data-science descriptive-statistics h2o machine-learning marketing mmm predictive-modeling puzzle rlanguage robyn visualization

3.6 match 233 stars 9.84 score 185 scripts 1 dependents

amanyiraho

dhis2r:Client for the 'DHIS2' Web API

Connect and pull data from a 'DHIS2 (District Health Information Software 2)' instance into R.

Maintained by Robinson Amanyiraho. Last updated 2 months ago.

api-client api-wrapper dhis2 dhis2-api

7.5 match 2 stars 4.70 score 6 scripts

matloff

dsld:Data Science Looks at Discrimination

Statistical and graphical tools for detecting and measuring discrimination and bias, be it racial, gender, age or other. Detection and remediation of bias in machine learning algorithms. 'Python' interfaces available.

Maintained by Norm Matloff. Last updated 1 months ago.

4.5 match 12 stars 7.81 score 35 scripts

ropensci

concstats:Market Structure, Concentration and Inequality Measures

Based on individual market shares of all participants in a market or space, the package offers a set of different structural and concentration measures frequently - and not so frequently - used in research and in practice. Measures can be calculated in groups or individually. The calculated measure or the resulting vector in table format should help practitioners make more informed decisions. Methods used in this package are from: 1. Chang, E. J., Guerra, S. M., de Souza Penaloza, R. A. & Tabak, B. M. (2005) "Banking concentration: the Brazilian case". 2. Cobham, A. and A. Summer (2013). "Is It All About the Tails? The Palma Measure of Income Inequality". 3. Garcia Alba Idunate, P. (1994). "Un Indice de dominancia para el analisis de la estructura de los mercados". 4. Ginevicius, R. and S. Cirba (2009). "Additive measurement of market concentration" <doi:10.3846/1611-1699.2009.10.191-198>. 5. Herfindahl, O. C. (1950), "Concentration in the steel industry" (PhD thesis). 6. Hirschmann, A. O. (1945), "National power and structure of foreign trade". 7. Melnik, A., O. Shy, and R. Stenbacka (2008), "Assessing market dominance" <doi:10.1016/j.jebo.2008.03.010>. 8. Palma, J. G. (2006). "Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces at Work". 9. Shannon, C. E. (1948). "A Mathematical Theory of Communication". 10. Simpson, E. H. (1949). "Measurement of Diversity" <doi:10.1038/163688a0>.

Maintained by Andreas Schneider. Last updated 1 years ago.

business-analytics competition concentration diversity inequality package-development

7.0 match 7 stars 5.02 score 15 scripts

r-spatial

qgisprocess:Use 'QGIS' Processing Algorithms

Provides seamless access to the 'QGIS' (<https://qgis.org>) processing toolbox using the standalone 'qgis_process' command-line utility. Both native and third-party (plugin) processing providers are supported. Beside referring data sources from file, also common objects from 'sf', 'terra' and 'stars' are supported. The native processing algorithms are documented by QGIS.org (2024) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.

Maintained by Floris Vanderhaeghe. Last updated 5 months ago.

3.5 match 210 stars 10.09 score 175 scripts

r-forge

RobAStBase:Robust Asymptotic Statistics

Base S4-classes and functions for robust asymptotic statistics.

Maintained by Matthias Kohl. Last updated 2 months ago.

7.0 match 4.96 score 64 scripts 4 dependents

carlganz

rintrojs:Wrapper for the 'Intro.js' Library

A wrapper for the 'Intro.js' library (For more info: <https://introjs.com/>). This package makes it easy to include step-by-step introductions, and clickable hints in a 'Shiny' application. It supports both static introductions in the UI, and programmatic introductions from the server-side.

Maintained by Carl Ganz. Last updated 1 years ago.

introjs shiny

3.6 match 134 stars 9.54 score 308 scripts 30 dependents

topepo

caret:Classification and Regression Training

Misc functions for training and plotting classification and regression models.

Maintained by Max Kuhn. Last updated 3 months ago.

1.8 match 1.6k stars 19.24 score 61k scripts 303 dependents

benbruyneel

proteinDiscover:ProteinDiscover

Provides an interface to the data contained in Proteome Discoverer (Thermo Scientific) results.

Maintained by Ben Bruyneel. Last updated 1 years ago.

mass-spectrometry proteomics proteomics-data-analysis

11.5 match 2 stars 3.00 score 2 scripts

rmgpanw

trud:Query the 'NHS TRUD API'

A convenient R interface to the 'National Health Service (NHS) Technology Reference Update Distribution (TRUD) API'. Retrieve available releases for items that you are subscribed to and download these with ease. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.

Maintained by Alasdair Warwick. Last updated 6 months ago.

api-wrapper ehr icd nhs snomed-ct

7.5 match 3 stars 4.61 score 3 scripts

kenkellner

jagsUI:A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses

A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.

Maintained by Ken Kellner. Last updated 1 months ago.

jags cpp

3.4 match 35 stars 10.02 score 1.4k scripts 7 dependents

bioc

bayNorm:Single-cell RNA sequencing data normalization

bayNorm is used for normalizing single-cell RNA-seq data.

Maintained by Wenhao Tang. Last updated 5 months ago.

immunooncology normalization rnaseq singlecell sequencing scrnaseq cpp openmp

5.2 match 9 stars 6.59 score 36 scripts

disohda

FDX:False Discovery Exceedance Controlling Multiple Testing Procedures

Multiple testing procedures for heterogeneous and discrete tests as described in Döhler and Roquain (2020) <doi:10.1214/20-EJS1771>. The main algorithms of the paper are available as continuous, discrete and weighted versions. They take as input the results of a test procedure from package 'DiscreteTests', or a set of observed p-values and their discrete support under their nulls. A shortcut function to obtain such p-values and supports is also provided, along with wrappers allowing to apply discrete procedures directly to data.

Maintained by Florian Junge. Last updated 4 months ago.

cpp

10.8 match 2 stars 3.15 score 1 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

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

ropensci

eia:API Wrapper for U.S. Energy Information Administration ('EIA') Open Data

Provides API access to data from the U.S. Energy Information Administration ('EIA') <https://www.eia.gov/>. Use of the EIA's API and this package requires a free API key obtainable at <https://www.eia.gov/opendata/register.php>. This package includes functions for searching the EIA data directory and returning time series and geoset time series datasets. Datasets returned by these functions are provided by default in a tidy format, or alternatively, in more raw formats. It also offers helper functions for working with EIA date strings and time formats and for inspecting different summaries of series metadata. The package also provides control over API key storage and caching of API request results.

Maintained by Matthew Hoff. Last updated 8 months ago.

eia eia-api energy-data energy-information-administration open-data

4.6 match 47 stars 7.30 score 35 scripts

rsquaredacademy

yahoofinancer:Fetch Data from Yahoo Finance API

Obtain historical and near real time data related to stocks, index and currencies from the Yahoo Finance API. This package is community maintained and is not officially supported by 'Yahoo'. The accuracy of data is only as correct as provided on <https://finance.yahoo.com/>.

Maintained by Aravind Hebbali. Last updated 2 months ago.

api api-wrapper finance market-data stock-market yahoo-finance yahoo-finance-api

7.5 match 16 stars 4.46 score 18 scripts

ropensci

gert:Simple Git Client for R

Simple git client for R based on 'libgit2' <https://libgit2.org> with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent.

Maintained by Jeroen Ooms. Last updated 4 months ago.

libgit2

2.3 match 154 stars 14.82 score 158 scripts 369 dependents

kjakobse

EpiForsk:Code Sharing at the Department of Epidemiological Research at Statens Serum Institut

This is a collection of assorted functions and examples collected from various projects. Currently we have functionalities for simplifying overlapping time intervals, Charlson comorbidity score constructors for Danish data, getting frequency for multiple variables, getting standardized output from logistic and log-linear regressions, sibling design linear regression functionalities a method for calculating the confidence intervals for functions of parameters from a GLM, Bayes equivalent for hypothesis testing with asymptotic Bayes factor, and several help functions for generalized random forest analysis using 'grf'.

Maintained by Kim Daniel Jakobsen. Last updated 1 years ago.

7.4 match 4.48 score 8 scripts

oobianom

nextGenShinyApps:Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools

Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts and style sheets are based on 'jQuery' <https://jquery.com/> and 'Bootstrap' <https://getbootstrap.com/>.

Maintained by Obinna Obianom. Last updated 8 months ago.

apps dashboard shiny

5.6 match 10 stars 5.95 score 59 scripts 1 dependents

matbmeijer

DemografixeR:Extrapolate Gender, Age and Nationality of a Name

Connects to the <https://genderize.io/>, <https://agify.io/> and <https://nationalize.io/> APIs to estimate gender, age and nationality of a first name.

Maintained by Matthias Brenninkmeijer. Last updated 5 years ago.

age-prediction api-wrapper demographics gender-classification nationality-predicter

7.5 match 5 stars 4.40 score 10 scripts

tidymodels

recipes:Preprocessing and Feature Engineering Steps for Modeling

A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.

Maintained by Max Kuhn. Last updated 5 days ago.

1.8 match 584 stars 18.71 score 7.2k scripts 380 dependents

vladimirholy

gasmodel:Generalized Autoregressive Score Models

Estimation, forecasting, and simulation of generalized autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013) <doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>. Model specification allows for various data types and distributions, different parametrizations, exogenous variables, joint and separate modeling of exogenous variables and dynamics, higher score and autoregressive orders, custom and unconditional initial values of time-varying parameters, fixed and bounded values of coefficients, and missing values. Model estimation is performed by the maximum likelihood method.

Maintained by Vladimír Holý. Last updated 1 years ago.

dcs gas time-series

6.0 match 14 stars 5.45 score 2 scripts

mhpob

matos:Interface with the Mid-Atlantic Acoustic Telemetry Observing System (MATOS)

This package provides HTML-scaping functions to interact with the MATOS website (https://matos.asascience.com/), allowing aggregation of data and the downloading and posting of files.

Maintained by Michael OBrien. Last updated 3 months ago.

animal-tracking api api-wrapper biotelemetry fish fisheries fisheries-research

7.5 match 3 stars 4.35 score 9 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 2 days ago.

ccte comptox ord

3.5 match 36 stars 9.41 score 90 scripts

sinhrks

ggfortify:Data Visualization Tools for Statistical Analysis Results

Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.

Maintained by Yuan Tang. Last updated 9 months ago.

2.3 match 529 stars 14.49 score 9.1k scripts 22 dependents

geco-bern

rsofun:The P-Model and BiomeE Modelling Framework

Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).

Maintained by Benjamin Stocker. Last updated 13 days ago.

dgvm growth modeling p-model simulation vegetation-dynamics fortran

3.7 match 26 stars 8.77 score 119 scripts

alexanderrobitzsch

miceadds:Some Additional Multiple Imputation Functions, Especially for 'mice'

Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are implemented. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>), substantive model compatible imputation (Bartlett et al., 2015, <doi:10.1177/0962280214521348>), and features for the generation of synthetic datasets (Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>; Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).

Maintained by Alexander Robitzsch. Last updated 15 days ago.

missing-data multiple-imputation openblas cpp

3.5 match 16 stars 9.16 score 542 scripts 9 dependents

marcinjurek

GPvecchia:Scalable Gaussian-Process Approximations

Fast scalable Gaussian process approximations, particularly well suited to spatial (aerial, remote-sensed) and environmental data, described in more detail in Katzfuss and Guinness (2017) <arXiv:1708.06302>. Package also contains a fast implementation of the incomplete Cholesky decomposition (IC0), based on Schaefer et al. (2019) <arXiv:1706.02205> and MaxMin ordering proposed in Guinness (2018) <arXiv:1609.05372>.

Maintained by Marcin Jurek. Last updated 1 years ago.

openblas cpp openmp

7.5 match 4.26 score 61 scripts 2 dependents

jefferis

nabor:Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions

An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). 'libnabo' has speed and space advantages over the 'ANN' library wrapped by package 'RANN'. 'nabor' includes a knn function that is designed as a drop-in replacement for 'RANN' function nn2. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.

Maintained by Gregory Jefferis. Last updated 5 years ago.

libnabo nearest-neighbors cpp

3.9 match 22 stars 8.21 score 104 scripts 34 dependents

r-lib

cpp11:A C++11 Interface for R's C Interface

Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.

Maintained by Davis Vaughan. Last updated 11 days ago.

cpp cpp11

1.8 match 212 stars 17.69 score 104 scripts 8.6k dependents

bioc

vsn:Variance stabilization and calibration for microarray data

The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Maintained by Wolfgang Huber. Last updated 5 months ago.

microarray onechannel twochannel preprocessing

3.8 match 8.49 score 924 scripts 51 dependents

oobianom

card.pro:Lightweight Modern & Responsive Card Component for 'shiny'

Responsive and modern 'HTML' card essentials for 'shiny' applications and dashboards. This novel card component in 'Bootstrap' provides a flexible and extensible content container with multiple variants and options for building robust 'R' based apps e.g for graph build or machine learning projects. The features rely on a combination of 'JQuery' <https://jquery.com> and 'CSS' styles to improve the card functionality.

Maintained by Obinna Obianom. Last updated 27 days ago.

5.6 match 5 stars 5.72 score 13 scripts

trnnick

MAPA:Multiple Aggregation Prediction Algorithm

Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure. For details see Kourentzes et al. (2014) <doi:10.1016/j.ijforecast.2013.09.006>.

Maintained by Nikolaos Kourentzes. Last updated 1 years ago.

4.1 match 16 stars 7.63 score 38 scripts 21 dependents

bioc

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Maintained by Changqing Wang. Last updated 5 days ago.

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread zlib curl bzip2 xz-utils cpp

3.9 match 31 stars 7.95 score 12 scripts

bioc

TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Maintained by Ge Tan. Last updated 4 days ago.

motifannotation generegulation motifdiscovery transcription alignment

2.5 match 28 stars 12.36 score 1.1k scripts 18 dependents

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 12 days ago.

gis leaflet-map spatial

1.8 match 821 stars 17.20 score 39k scripts 178 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 19 hours ago.

oceanography fortran cpp

2.0 match 146 stars 15.42 score 4.2k scripts 18 dependents

doubleml

DoubleML:Double Machine Learning in R

Implementation of the double/debiased machine learning framework of Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear regression models, partially linear instrumental variable regression models, interactive regression models and interactive instrumental variable regression models. 'DoubleML' allows estimation of the nuisance parts in these models by machine learning methods and computation of the Neyman orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the 'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on the 'R6' package is very flexible. More information available in the publication in the Journal of Statistical Software: <doi:10.18637/jss.v108.i03>.

Maintained by Philipp Bach. Last updated 4 months ago.

causal-inference data-science double-machine-learning econometrics machine-learning mlr3 statistics

3.4 match 137 stars 9.17 score 267 scripts 1 dependents

bioc

csaw:ChIP-Seq Analysis with Windows

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Maintained by Aaron Lun. Last updated 2 months ago.

multiplecomparison chipseq normalization sequencing coverage genetics annotation differentialpeakcalling curl bzip2 xz-utils zlib cpp

3.7 match 8.32 score 498 scripts 7 dependents