R-universe search: needs:httr2

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 12 days ago.

documentation-tool

734 stars 18.46 score 588 scripts 162 dependents

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 26 days ago.

github setup

869 stars 17.54 score 5.6k scripts 336 dependents

bioc

biomaRt:Interface to BioMart databases (i.e. Ensembl)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Maintained by Mike Smith. Last updated 17 days ago.

annotation bioconductor biomart ensembl

38 stars 15.99 score 13k scripts 230 dependents

r-lib

gh:'GitHub' 'API'

Minimal client to access the 'GitHub' 'API'.

Maintained by Gábor Csárdi. Last updated 2 months ago.

github github-api

224 stars 15.55 score 444 scripts 401 dependents

ropensci

osmdata:Import 'OpenStreetMap' Data as Simple Features or Spatial Objects

Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.

Maintained by Mark Padgham. Last updated 2 months ago.

open0street0map openstreetmap overpass0api osm cpp osm-data overpass-api peer-reviewed cpp

322 stars 14.53 score 2.8k scripts 14 dependents

bioc

TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Maintained by Tiago Chedraoui Silva. Last updated 1 months ago.

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

310 stars 14.47 score 1.6k scripts 6 dependents

doi-usgs

dataRetrieval:Retrieval Functions for USGS and EPA Hydrology and Water Quality Data

Collection of functions to help retrieve U.S. Geological Survey and U.S. Environmental Protection Agency water quality and hydrology data from web services. Data are discovered from National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.

Maintained by Laura DeCicco. Last updated 5 days ago.

usgs

286 stars 14.16 score 1.7k scripts 15 dependents

bioc

GEOquery:Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Maintained by Sean Davis. Last updated 5 months ago.

microarray dataimport onechannel twochannel sage bioconductor bioinformatics data-science genomics ncbi-geo

93 stars 13.48 score 4.1k scripts 45 dependents

business-science

tidyquant:Tidy Quantitative Financial Analysis

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

Maintained by Matt Dancho. Last updated 2 months ago.

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

872 stars 13.34 score 5.2k scripts

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

79 stars 13.05 score 1.4k scripts 46 dependents

ropensci

piggyback:Managing Larger Data on a GitHub Repository

Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.

Maintained by Carl Boettiger. Last updated 4 months ago.

data-store git-lfs peer-reviewed

187 stars 12.98 score 187 scripts 12 dependents

tidyverse

ellmer:Chat with Large Language Models

Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.

Maintained by Hadley Wickham. Last updated 3 days ago.

407 stars 12.94 score 98 scripts 8 dependents

bioc

minfi:Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Maintained by Kasper Daniel Hansen. Last updated 4 months ago.

immunooncology dnamethylation differentialmethylation epigenetics microarray methylationarray multichannel twochannel dataimport normalization preprocessing qualitycontrol

60 stars 12.82 score 996 scripts 27 dependents

bioc

ggbio:Visualization tools for genomic data

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

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

111 stars 12.23 score 734 scripts 16 dependents

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 3 days ago.

distance openstreetmap router shortest-paths street-networks cpp

129 stars 11.52 score 229 scripts 4 dependents

r4ss

r4ss:R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Maintained by Ian G. Taylor. Last updated 20 days ago.

fisheries fisheries-stock-assessment stock-synthesis

43 stars 11.38 score 1.0k scripts 2 dependents

doi-usgs

nhdplusTools:NHDPlus Tools

Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.

Maintained by David Blodgett. Last updated 1 months ago.

87 stars 11.38 score 348 scripts 5 dependents

ropensci

biomartr:Genomic Data Retrieval

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Maintained by Hajk-Georg Drost. Last updated 2 months ago.

biomart genomic-data-retrieval annotation-retrieval database-retrieval ncbi ensembl biological-data-retrieval ensembl-servers genome genome-annotation genome-retrieval genomics meta-analysis metagenomics ncbi-genbank peer-reviewed proteome sequenced-genomes

218 stars 11.35 score 129 scripts 3 dependents

paws-r

paws:Amazon Web Services Software Development Kit

Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 11.25 score 177 scripts 12 dependents

ropengov

eurostat:Tools for Eurostat Open Data

Tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Maintained by Leo Lahti. Last updated 1 months ago.

ropengov eurostat eurostat-data

242 stars 11.07 score 892 scripts 4 dependents

paws-r

paws.common:Paws Low-Level Amazon Web Services API

Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk cpp

332 stars 11.07 score 39 dependents

michelnivard

gptstudio:Use Large Language Models Directly in your Development Environment

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Maintained by James Wade. Last updated 5 days ago.

chatgpt gpt-3 rstudio rstudio-addin

930 stars 10.85 score 43 scripts 1 dependents

jimmyday12

fitzRoy:Easily Scrape and Process AFL Data

An easy package for scraping and processing Australia Rules Football (AFL) data. 'fitzRoy' provides a range of functions for accessing publicly available data from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and 'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing, cleaning and transformation of this data into formats that can be used for analysis.

Maintained by James Day. Last updated 10 days ago.

136 stars 10.72 score 324 scripts

doi-usgs

EGRET:Exploration and Graphics for RivEr Trends

Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).

Maintained by Laura DeCicco. Last updated 4 months ago.

usgs water-quality water-quality-data

90 stars 10.67 score 362 scripts 1 dependents

bioc

tximeta:Transcript Quantification Import with Automatic Metadata

Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

Maintained by Michael Love. Last updated 2 months ago.

annotation genomeannotation dataimport preprocessing rnaseq singlecell transcriptomics transcription geneexpression functionalgenomics reproducibleresearch reportwriting immunooncology

67 stars 10.58 score 466 scripts 1 dependents

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 1 months ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

33 stars 10.56 score 115 scripts 2 dependents

ropensci

gutenbergr:Download and Process Public Domain Works from Project Gutenberg

Download and process public domain works in the Project Gutenberg collection <https://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.

Maintained by Jon Harmon. Last updated 3 months ago.

peer-reviewed

105 stars 10.50 score 1.1k scripts 1 dependents

mlverse

chattr:Interact with Large Language Models in 'RStudio'

Enables user interactivity with large-language models ('LLM') inside the 'RStudio' integrated development environment (IDE). The user can interact with the model using the 'shiny' app included in this package, or directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub' 'Copilot', and 'LlamaGPT'.

Maintained by Edgar Ruiz. Last updated 2 months ago.

224 stars 10.36 score 71 scripts 1 dependents

bioc

pRoloc:A unifying bioinformatics framework for spatial proteomics

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Maintained by Lisa Breckels. Last updated 4 days ago.

immunooncology proteomics massspectrometry classification clustering qualitycontrol bioconductor proteomics-data spatial-proteomics visualisation openblas cpp

15 stars 10.31 score 101 scripts 2 dependents

bioc

EDASeq:Exploratory Data Analysis and Normalization for RNA-Seq

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

Maintained by Davide Risso. Last updated 5 months ago.

immunooncology sequencing rnaseq preprocessing qualitycontrol differentialexpression

5 stars 10.24 score 594 scripts 9 dependents

bioc

cBioPortalData:Exposes and Makes Available Data from the cBioPortal Web Resources

The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.

Maintained by Marcel Ramos. Last updated 10 days ago.

software infrastructure thirdpartyclient bioconductor-package nci-itcr u24ca289073

33 stars 10.17 score 147 scripts 4 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 1 months ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

182 stars 10.17 score 252 scripts

dslc-io

tidytuesdayR:Access the Weekly 'TidyTuesday' Project Dataset

'TidyTuesday' is a project by the 'Data Science Learning Community' in which they post a weekly dataset in a public data repository (<https://github.com/rfordatascience/tidytuesday>) for people to analyze and visualize. This package provides the tools to easily download this data and the description of the source.

Maintained by Jon Harmon. Last updated 5 days ago.

77 stars 10.13 score 3.0k scripts

8-bit-sheep

googleAnalyticsR:Google Analytics API into R

Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, User Activity API GA4's Data API and Admin API and Multi-Channel Funnel API.

Maintained by Erik Grönroos. Last updated 7 months ago.

analytics api google googleanalyticsr googleauthr

262 stars 10.11 score 680 scripts 1 dependents

ropensci

vcr:Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Maintained by Scott Chamberlain. Last updated 27 days ago.

http https api web-services curl mock mocking http-mocking testing testing-tools tdd unit-testing vcr

77 stars 10.06 score 165 scripts

bioc

BiocCheck:Bioconductor-specific package checks

BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.

Maintained by Marcel Ramos. Last updated 1 months ago.

infrastructure bioconductor-package core-services

8 stars 10.03 score 114 scripts 6 dependents

bioc

goseq:Gene Ontology analyser for RNA-seq and other length biased data

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Maintained by Federico Marini. Last updated 5 months ago.

immunooncology sequencing go geneexpression transcription rnaseq differentialexpression annotation genesetenrichment kegg pathways software

2 stars 9.97 score 636 scripts 9 dependents

r-lib

ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More

Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.

Maintained by Malcolm Barrett. Last updated 3 years ago.

165 stars 9.92 score 196 scripts 14 dependents

bioc

RUVSeq:Remove Unwanted Variation from RNA-Seq Data

This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

Maintained by Davide Risso. Last updated 5 months ago.

immunooncology differentialexpression preprocessing rnaseq software

13 stars 9.91 score 482 scripts 5 dependents

bioc

OmnipathR:OmniPath web service client and more

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

Maintained by Denes Turei. Last updated 1 months ago.

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

130 stars 9.90 score 226 scripts 2 dependents

bioc

methylumi:Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Maintained by Sean Davis. Last updated 5 months ago.

dnamethylation twochannel preprocessing qualitycontrol cpgisland

9 stars 9.90 score 89 scripts 9 dependents

bioc

GenVisR:Genomic Visualizations in R

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

Maintained by Zachary Skidmore. Last updated 5 months ago.

infrastructure datarepresentation classification dnaseq

217 stars 9.87 score 76 scripts

cjvanlissa

worcs:Workflow for Open Reproducible Code in Science

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

Maintained by Caspar J. Van Lissa. Last updated 2 days ago.

83 stars 9.77 score 59 scripts 1 dependents

paws-r

paws.storage:'Amazon Web Services' Storage Services

Interface to 'Amazon Web Services' storage services, including 'Simple Storage Service' ('S3') and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.75 score 17 scripts 18 dependents

appsilon

shiny.telemetry:'Shiny' App Usage Telemetry

Enables instrumentation of 'Shiny' apps for tracking user session events such as input changes, browser type, and session duration. These events can be sent to any of the available storage backends and analyzed using the included 'Shiny' app to gain insights about app usage and adoption.

Maintained by André Veríssimo. Last updated 4 months ago.

analytics rhinoverse shiny

67 stars 9.69 score 29 scripts

bioc

txdbmaker:Tools for making TxDb objects from genomic annotations

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Maintained by H. Pagès. Last updated 4 months ago.

infrastructure dataimport annotation genomeannotation genomeassembly genetics sequencing bioconductor-package core-package

3 stars 9.68 score 92 scripts 87 dependents

bioc

pcaExplorer:Interactive Visualization of RNA-seq Data Using a Principal Components Approach

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Maintained by Federico Marini. Last updated 3 months ago.

immunooncology visualization rnaseq dimensionreduction principalcomponent qualitycontrol gui reportwriting shinyapps bioconductor principal-components reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome user-friendly

56 stars 9.63 score 180 scripts

ropensci

tidyhydat:Extract and Tidy Canadian 'Hydrometric' Data

Provides functions to access historical and real-time national 'hydrometric' data from Water Survey of Canada data sources (<https://dd.weather.gc.ca/hydrometric/csv/> and <https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>) and then applies tidy data principles.

Maintained by Sam Albers. Last updated 20 days ago.

citz government-data hydrology hydrometrics tidy-data water-resources

71 stars 9.59 score 202 scripts 3 dependents

bioc

recount:Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Maintained by Leonardo Collado-Torres. Last updated 4 months ago.

coverage differentialexpression geneexpression rnaseq sequencing software dataimport immunooncology annotation-agnostic bioconductor count derfinder deseq2 exon gene human illumina junction recount

41 stars 9.57 score 498 scripts 3 dependents

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

163 stars 9.45 score 35 scripts

ropensci

DataPackageR:Construct Reproducible Analytic Data Sets as R Packages

A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.

Maintained by Dave Slager. Last updated 7 months ago.

peer-reviewed reproducibility

156 stars 9.38 score 72 scripts

nealrichardson

httptest2:Test Helpers for 'httr2'

Testing and documenting code that communicates with remote servers can be painful. This package helps with writing tests for packages that use 'httr2'. It enables testing all of the logic on the R sides of the API without requiring access to the remote service, and it also allows recording real API responses to use as test fixtures. The ability to save responses and load them offline also enables writing vignettes and other dynamic documents that can be distributed without access to a live server.

Maintained by Neal Richardson. Last updated 9 months ago.

http mock testing

33 stars 9.37 score 95 scripts 1 dependents

briencj

asremlPlus:Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 1 months ago.

asreml mixed-models

19 stars 9.37 score 200 scripts

hauselin

ollamar:'Ollama' Language Models

An interface to easily run local language models with 'Ollama' <https://ollama.com> server and API endpoints (see <https://github.com/ollama/ollama/blob/main/docs/api.md> for details). It lets you run open-source large language models locally on your machine.

Maintained by Hause Lin. Last updated 7 days ago.

ai api llm llms ollama ollama-api

89 stars 9.32 score 74 scripts 5 dependents

bioc

GenomicInteractions:Utilities for handling genomic interaction data

Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.

Maintained by Liz Ing-Simmons. Last updated 5 months ago.

software infrastructure dataimport datarepresentation hic

7 stars 9.31 score 162 scripts 5 dependents

bioc

IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.

geneexpression transcription alternativesplicing differentialexpression differentialsplicing visualization statisticalmethod transcriptomevariant biomedicalinformatics functionalgenomics systemsbiology transcriptomics rnaseq annotation functionalprediction geneprediction dataimport multiplecomparison batcheffect immunooncology

108 stars 9.26 score 125 scripts

mapme-initiative

mapme.biodiversity:Efficient Monitoring of Global Biodiversity Portfolios

Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.

Maintained by Darius A. Görgen. Last updated 3 days ago.

environment eo gis mapme spatial sustainability

35 stars 9.24 score 287 scripts

gojiplus

tuber:Client for the YouTube API

Get comments posted on YouTube videos, information on how many times a video has been liked, search for videos with particular content, and much more. You can also scrape captions from a few videos. To learn more about the YouTube API, see <https://developers.google.com/youtube/v3/>.

Maintained by Gaurav Sood. Last updated 6 days ago.

access-youtube caption video youtube youtube-api youtube-oauth

184 stars 9.21 score 206 scripts

atlasoflivingaustralia

galah:Biodiversity Data from the GBIF Node Network

The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.

Maintained by Martin Westgate. Last updated 2 months ago.

43 stars 9.17 score 275 scripts 1 dependents

paws-r

paws.security.identity:'Amazon Web Services' Security, Identity, & Compliance Services

Interface to 'Amazon Web Services' security, identity, and compliance services, including the 'Identity & Access Management' ('IAM') service for managing access to services and resources, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.17 score 15 dependents

paws-r

paws.compute:'Amazon Web Services' Compute Services

Interface to 'Amazon Web Services' compute services, including 'Elastic Compute Cloud' ('EC2'), 'Lambda' functions-as-a-service, containers, batch processing, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.12 score 16 dependents

paws-r

paws.management:'Amazon Web Services' Management & Governance Services

Interface to 'Amazon Web Services' management and governance services, including 'CloudWatch' application and infrastructure monitoring, 'Auto Scaling' for automatically scaling resources, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.09 score 1 scripts 15 dependents

bioc

OUTRIDER:OUTRIDER - OUTlier in RNA-Seq fInDER

Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.

Maintained by Christian Mertes. Last updated 5 months ago.

immunooncology rnaseq transcriptomics alignment sequencing geneexpression genetics count-data diagnostics expression-analysis mendelian-genetics outlier-detection rna-seq openblas cpp

50 stars 9.07 score 110 scripts 1 dependents

paws-r

paws.analytics:'Amazon Web Services' Analytics Services

Interface to 'Amazon Web Services' 'analytics' services, including 'Elastic MapReduce' 'Hadoop' and 'Spark' big data service, 'Elasticsearch' search engine, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.07 score 13 dependents

paws-r

paws.database:'Amazon Web Services' Database Services

Interface to 'Amazon Web Services' database services, including 'Relational Database Service' ('RDS'), 'DynamoDB' 'NoSQL' database, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.07 score 3 scripts 13 dependents

paws-r

paws.application.integration:'Amazon Web Services' Application Integration Services

Interface to 'Amazon Web Services' application integration services, including 'Simple Queue Service' ('SQS') message queue, 'Simple Notification Service' ('SNS') publish/subscribe messaging, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.06 score 14 dependents

paws-r

paws.machine.learning:'Amazon Web Services' Machine Learning Services

Interface to 'Amazon Web Services' machine learning services, including 'SageMaker' managed machine learning service, natural language processing, speech recognition, translation, and more <https://aws.amazon.com/machine-learning/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.05 score 14 dependents

paws-r

paws.networking:'Amazon Web Services' Networking & Content Delivery Services

Interface to 'Amazon Web Services' networking and content delivery services, including 'Route 53' Domain Name System service, 'CloudFront' content delivery, load balancing, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.05 score 13 dependents

paws-r

paws.developer.tools:'Amazon Web Services' Developer Tools Services

Interface to 'Amazon Web Services' developer tools services, including version control, continuous integration and deployment, and more <https://aws.amazon.com/products/developer-tools/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.03 score 14 dependents

bioc

scPipe:Pipeline for single cell multi-omic data pre-processing

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.

Maintained by Shian Su. Last updated 3 months ago.

immunooncology software sequencing rnaseq geneexpression singlecell visualization sequencematching preprocessing qualitycontrol genomeannotation dataimport curl bzip2 xz-utils zlib cpp

68 stars 9.02 score 84 scripts

paws-r

paws.cost.management:'Amazon Web Services' Cost Management Services

Interface to 'Amazon Web Services' cost management services, including cost and usage reports, budgets, pricing, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.02 score 13 dependents

paws-r

paws.customer.engagement:'Amazon Web Services' Customer Engagement Services

Interface to 'Amazon Web Services' customer engagement services, including 'Simple Email Service', 'Connect' contact center service, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.01 score 13 dependents

paws-r

paws.end.user.computing:'Amazon Web Services' End User Computing Services

Interface to 'Amazon Web Services' end user computing services, including collaborative document editing, mobile intranet, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 9.00 score 13 dependents

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 1 months ago.

immunooncology normalization preprocessing qualitycontrol geneexpression rnaseq software transcriptomics sequencing singlecell coverage

53 stars 9.00 score 104 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.

26 stars 8.99 score 78 scripts 1 dependents

pharmar

riskmetric:Risk Metrics to Evaluating R Packages

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

Maintained by Eli Miller. Last updated 7 days ago.

166 stars 8.98 score 43 scripts

cjbarrie

academictwitteR:Access the Twitter Academic Research Product Track V2 API Endpoint

Package to query the Twitter Academic Research Product Track, providing access to full-archive search and other v2 API endpoints. Functions are written with academic research in mind. They provide flexibility in how the user wishes to store collected data, and encourage regular storage of data to mitigate loss when collecting large volumes of tweets. They also provide workarounds to manage and reshape the format in which data is provided on the client side.

Maintained by Christopher Barrie. Last updated 2 years ago.

twitter twitter-api

275 stars 8.94 score 177 scripts

guangchuangyu

badger:Badge for R Package

Query information and generate badge for using in README and GitHub Pages.

Maintained by Guangchuang Yu. Last updated 9 months ago.

badge

197 stars 8.92 score 225 scripts 5 dependents

usa-npn

rnpn:Interface to the National 'Phenology' Network 'API'

Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.

Maintained by Jeff Switzer. Last updated 5 days ago.

data national-phenology-network phenology species web-api

21 stars 8.91 score 109 scripts

ajrgodfrey

BrailleR:Improved Access for Blind Users

Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.

Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.

123 stars 8.90 score 143 scripts

ropensci

codemetar:Generate 'CodeMeta' Metadata for R Packages

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

Maintained by Carl Boettiger. Last updated 2 months ago.

metadata codemeta ropensci citation credit linked-data json-ld peer-reviewed

68 stars 8.90 score 34 scripts 6 dependents

bioc

motifbreakR:A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).

Maintained by Simon Gert Coetzee. Last updated 5 months ago.

chipseq visualization motifannotation transcription

28 stars 8.89 score 103 scripts

pik-piam

remind2:The REMIND R package (2nd generation)

Contains the REMIND-specific routines for data and model output manipulation.

Maintained by Renato Rodrigues. Last updated 3 days ago.

8.87 score 161 scripts 5 dependents

dmi3kno

polite:Be Nice on the Web

Be responsible when scraping data from websites by following polite principles: introduce yourself, ask for permission, take slowly and never ask twice.

Maintained by Dmytro Perepolkin. Last updated 2 years ago.

crawler memoise rate-limiter robotstxt rvest scraper webscraping

327 stars 8.86 score 596 scripts 5 dependents

bioc

AnVIL:Bioconductor on the AnVIL compute environment

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Maintained by Marcel Ramos. Last updated 1 months ago.

infrastructure

8.85 score 250 scripts 11 dependents

fmichonneau

foghorn:Summarize CRAN Check Results in the Terminal

The CRAN check results and where your package stands in the CRAN submission queue in your R terminal.

Maintained by Francois Michonneau. Last updated 9 months ago.

feedback

56 stars 8.76 score 21 scripts

bioc

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

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

Maintained by Jianhong Ou. Last updated 3 months ago.

annotation chipseq chipchip

8.75 score 584 scripts 6 dependents

cynkra

fledge:Smoother Change Tracking and Versioning for R Packages

Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.

Maintained by Kirill Müller. Last updated 3 months ago.

changelog git package-creation

188 stars 8.73 score 10 scripts

ss3sim

ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis

A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.

Maintained by Kelli F. Johnson. Last updated 5 months ago.

fisheries simulation stock-synthesis

39 stars 8.72 score 149 scripts

bioc

memes:motif matching, comparison, and de novo discovery using the MEME Suite

A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.

Maintained by Spencer Nystrom. Last updated 5 months ago.

dataimport functionalgenomics generegulation motifannotation motifdiscovery sequencematching software

50 stars 8.69 score 117 scripts 1 dependents

bioc

trackViewer:A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Maintained by Jianhong Ou. Last updated 4 days ago.

visualization

8.68 score 145 scripts 2 dependents

ropensci

comtradr:Interface with the United Nations Comtrade API

Interface with and extract data from the United Nations 'Comtrade' API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.

Maintained by Paul Bochtler. Last updated 5 months ago.

api comtrade peer-reviewed supply-chain

66 stars 8.67 score 70 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

65 stars 8.65 score 128 scripts

bioc

QuasR:Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Maintained by Michael Stadler. Last updated 1 months ago.

genetics preprocessing sequencing chipseq rnaseq methylseq coverage alignment qualitycontrol immunooncology curl bzip2 xz-utils zlib cpp

6 stars 8.63 score 79 scripts 1 dependents

bioc

FRASER:Find RAre Splicing Events in RNA-Seq Data

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Maintained by Christian Mertes. Last updated 5 months ago.

rnaseq alternativesplicing sequencing software genetics coverage aberrant-splicing diagnostics outlier-detection rare-disease rna-seq splicing openblas cpp

44 stars 8.53 score 155 scripts

simonpcouch

chores:A Collection of Large Language Model Assistants

Provides a collection of ergonomic large language model assistants designed to help you complete repetitive, hard-to-automate tasks quickly. After selecting some code, press the keyboard shortcut you've chosen to trigger the package app, select an assistant, and watch your chore be carried out. While the package ships with a number of chore helpers for R package development, users can create custom helpers just by writing some instructions in a markdown file.

Maintained by Simon Couch. Last updated 1 months ago.

101 stars 8.44 score 6 scripts 1 dependents

bioc

UniProt.ws:R Interface to UniProt Web Services

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.

Maintained by Marcel Ramos. Last updated 3 months ago.

annotation infrastructure go kegg biocarta bioconductor-package core-package

4 stars 8.38 score 167 scripts 4 dependents

jbgruber

rollama:Communicate with 'Ollama' to Run Large Language Models Locally

Wraps the 'Ollama' <https://ollama.com> API, which can be used to communicate with generative large language models locally.

Maintained by Johannes B. Gruber. Last updated 2 months ago.

110 stars 8.36 score 52 scripts

posit-dev

shinylive:Run 'shiny' Applications in the Browser

Exporting 'shiny' applications with 'shinylive' allows you to run them entirely in a web browser, without the need for a separate R server. The traditional way of deploying 'shiny' applications involves in a separate server and client: the server runs R and 'shiny', and clients connect via the web browser. When an application is deployed with 'shinylive', R and 'shiny' run in the web browser (via 'webR'): the browser is effectively both the client and server for the application. This allows for your 'shiny' application exported by 'shinylive' to be hosted by a static web server.

Maintained by Barret Schloerke. Last updated 5 months ago.

187 stars 8.35 score 194 scripts

mrc-ide

orderly2:Orderly Next Generation

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Maintained by Rich FitzJohn. Last updated 3 months ago.

8 stars 8.30 score 49 scripts 2 dependents

bioc

rols:An R interface to the Ontology Lookup Service

The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.

Maintained by Laurent Gatto. Last updated 5 months ago.

immunooncology software annotation massspectrometry go

11 stars 8.30 score 89 scripts 5 dependents

bioc

GeneTonic:Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Maintained by Federico Marini. Last updated 3 months ago.

gui geneexpression software transcription transcriptomics visualization differentialexpression pathways reportwriting genesetenrichment annotation go shinyapps bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression pathway-analysis reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome user-friendly

77 stars 8.28 score 37 scripts 1 dependents

bioc

crisprDesign:Comprehensive design of CRISPR gRNAs for nucleases and base editors

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Maintained by Jean-Philippe Fortin. Last updated 26 days ago.

crispr functionalgenomics genetarget bioconductor bioconductor-package crispr-cas9 crispr-design crispr-target genomics-analysis grna grna-sequence grna-sequences sgrna sgrna-design

22 stars 8.28 score 80 scripts 3 dependents

ramikrispin

coronavirus:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.

Maintained by Rami Krispin. Last updated 2 years ago.

covid-19 covid19 covid19-data dataset

499 stars 8.25 score 716 scripts

ropenspain

climaemet:Climate AEMET Tools

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

Maintained by Diego Hernangómez. Last updated 6 days ago.

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

42 stars 8.25 score 59 scripts

nixtla

nixtlar:A Software Development Kit for 'Nixtla''s 'TimeGPT'

A Software Development Kit for working with 'Nixtla''s 'TimeGPT', a foundation model for time series forecasting. 'API' is an acronym for 'application programming interface'; this package allows users to interact with 'TimeGPT' via the 'API'. You can set and validate 'API' keys and generate forecasts via 'API' calls. It is compatible with 'tsibble' and base R. For more details visit <https://docs.nixtla.io/>.

Maintained by Mariana Menchero. Last updated 1 months ago.

32 stars 8.19 score 38 scripts

jbgruber

atrrr:Wrapper for the 'AT' Protocol Behind 'Bluesky'

Wraps the 'AT' Protocol (Authenticated Transfer Protocol) behind 'Bluesky' <https://bsky.social>. Functions can be used for, among others, retrieving posts and followers from the network or posting content.

Maintained by Johannes B. Gruber. Last updated 21 days ago.

atproto bluesky

28 stars 8.07 score 38 scripts

r-arcgis

arcgislayers:An Interface to ArcGIS Data Services

Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or 'ArcGIS Platform' to read, write, publish, or manage vector and raster data via ArcGIS location services REST API endpoints <https://developers.arcgis.com/rest/>.

Maintained by Josiah Parry. Last updated 13 days ago.

arcgis esri gis r-spatial

50 stars 8.07 score 38 scripts 4 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 8 hours ago.

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

33 stars 8.04 score 12 scripts

mazamascience

MazamaSpatialUtils:Spatial Data Download and Utility Functions

A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)

Maintained by Jonathan Callahan. Last updated 5 months ago.

5 stars 8.01 score 282 scripts 2 dependents

epiverse-trace

sivirep:Data Wrangling and Automated Reports from 'SIVIGILA' Source

Data wrangling, pre-processing, and generating automated reports from Colombia's epidemiological surveillance system, 'SIVIGILA' <https://portalsivigila.ins.gov.co/>. It provides a customizable R Markdown template for analysis and automatic generation of epidemiological reports that can be adapted to local, regional, and national contexts. This tool offers a standardized and reproducible workflow that helps to reduce manual labor and potential errors in report generation, improving their efficiency and consistency.

Maintained by Geraldine Gómez-Millán. Last updated 1 months ago.

colombia epidemiological-surveillance epiverse public-health

42 stars 8.00 score 21 scripts

bioc

netZooR:Unified methods for the inference and analysis of gene regulatory networks

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

Maintained by Tara Eicher. Last updated 13 days ago.

networkinference network generegulation geneexpression transcription microarray graphandnetwork gene-regulatory-network transcription-factors

105 stars 7.98 score

scasanova

f1dataR:Access Formula 1 Data

Obtain Formula 1 data via the 'Jolpica API' <https://jolpi.ca> and the unofficial API <https://www.formula1.com/en/timing/f1-live> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.

Maintained by Santiago Casanova. Last updated 4 days ago.

f1 formula1 sports-data

60 stars 7.97 score 26 scripts

ropensci

osmplotr:Bespoke Images of 'OpenStreetMap' Data

Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.

Maintained by Mark Padgham. Last updated 1 months ago.

data-visualisation highlighting-clusters openstreetmap osm overpass overpass-api peer-reviewed

139 stars 7.97 score 80 scripts

ropenspain

spanishoddata:Get Spanish Origin-Destination Data

Gain seamless access to origin-destination (OD) data from the Spanish Ministry of Transport, hosted at <https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>. This package simplifies the management of these large datasets by providing tools to download zone boundaries, handle associated origin-destination data, and process it efficiently with the 'duckdb' database interface. Local caching minimizes repeated downloads, streamlining workflows for researchers and analysts. Extensive documentation is available at <https://ropenspain.github.io/spanishoddata/index.html>, offering guides on creating static and dynamic mobility flow visualizations and transforming large datasets into analysis-ready formats.

Maintained by Egor Kotov. Last updated 10 days ago.

cdr data data-package mobile-telephone-data mobility origin-destination

35 stars 7.92 score 14 scripts

bioc

biocthis:Automate package and project setup for Bioconductor packages

This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

Maintained by Leonardo Collado-Torres. Last updated 10 days ago.

software reportwriting actions bioconductor biocthis github styler usethis

51 stars 7.90 score 4 scripts 1 dependents

edubruell

tidyllm:Tidy Integration of Large Language Models

A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Gemini','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.

Maintained by Eduard Brüll. Last updated 3 days ago.

70 stars 7.87 score 26 scripts

tbep-tech

tbeptools:Data and Indicators for the Tampa Bay Estuary Program

Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.

Maintained by Marcus Beck. Last updated 3 days ago.

data-analysis tampa-bay tbep water-quality

10 stars 7.86 score 133 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 2 months ago.

12 stars 7.81 score 35 scripts

bioc

Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Maintained by Nan Xiao. Last updated 5 months ago.

software dataimport datarepresentation featureextraction cheminformatics biomedicalinformatics proteomics go systemsbiology bioconductor bioinformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

37 stars 7.81 score 29 scripts

bioc

hermes:Preprocessing, analyzing, and reporting of RNA-seq data

Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.

Maintained by Daniel Sabanés Bové. Last updated 5 months ago.

rnaseq differentialexpression normalization preprocessing qualitycontrol rna-seq statistical-engineering

11 stars 7.77 score 48 scripts 1 dependents

edjnet

tidywikidatar:Explore 'Wikidata' Through Tidy Data Frames

Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local database.

Maintained by Giorgio Comai. Last updated 8 months ago.

wikidata

26 stars 7.76 score 46 scripts 2 dependents

mazamascience

MazamaCoreUtils:Utility Functions for Production R Code

A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, cache management and date-time parsing. Functions for date-time parsing and formatting require that time zones be specified explicitly, avoiding a common source of error when working with environmental time series.

Maintained by Jonathan Callahan. Last updated 4 months ago.

4 stars 7.76 score 119 scripts 5 dependents

bioc

LACE:Longitudinal Analysis of Cancer Evolution (LACE)

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

Maintained by Davide Maspero. Last updated 16 days ago.

biomedicalinformatics singlecell somaticmutation

15 stars 7.75 score 3 scripts

bioc

DEXSeq:Inference of differential exon usage in RNA-Seq

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Maintained by Alejandro Reyes. Last updated 1 months ago.

immunooncology sequencing rnaseq differentialexpression alternativesplicing differentialsplicing geneexpression visualization

7.75 score 330 scripts 6 dependents

bioc

wateRmelon:Illumina DNA methylation array normalization and metrics

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Maintained by Leo C Schalkwyk. Last updated 4 months ago.

dnamethylation microarray twochannel preprocessing qualitycontrol

7.73 score 247 scripts 2 dependents

cmu-delphi

epidatr:Client for Delphi's 'Epidata' API

The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.

Maintained by David Weber. Last updated 11 days ago.

5 stars 7.71 score 114 scripts

icarda-git

QBMS:Query the Breeding Management System(s)

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

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

8 stars 7.70 score 33 scripts 1 dependents

bioc

phantasus:Visual and interactive gene expression analysis

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Maintained by Alexey Sergushichev. Last updated 5 months ago.

geneexpression gui visualization datarepresentation transcriptomics rnaseq microarray normalization clustering differentialexpression principalcomponent immunooncology

43 stars 7.68 score 15 scripts

carpentries

sandpaper:Create and Curate Carpentries Lessons

We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.

Maintained by Robert Davey. Last updated 2 months ago.

carpentries carpentries-infrastructure carpentries-workbench lesson-template lessons markdown static-site-generator

44 stars 7.68 score 8 scripts

vosonlab

vosonSML:Collecting Social Media Data and Generating Networks for Analysis

A suite of easy to use functions for collecting social media data and generating networks for analysis. Supports Mastodon, YouTube, Reddit and Web 1.0 data sources.

Maintained by Bryan Gertzel. Last updated 8 months ago.

hyperlink mastodon network-graph reddit sna social-media social-network-analysis voson youtube

79 stars 7.67 score 66 scripts 1 dependents

bioc

BiocPkgTools:Collection of simple tools for learning about Bioconductor Packages

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

Maintained by Sean Davis. Last updated 27 days ago.

software infrastructure bioconductor metadata

21 stars 7.67 score 68 scripts

sciviews

SciViews:'SciViews' - Data Processing and Visualization with the 'SciViews::R' Dialect

The 'SciViews::R' dialect provides a set of functions that streamlines data input, process, analysis and visualization especially, but not exclusively, for beginners or occasional users. It mixes base R and tidyverse, plus another set of CRAN packages for an easy and coherent use of R.

Maintained by Philippe Grosjean. Last updated 7 months ago.

sciviews

8 stars 7.62 score 116 scripts 1 dependents

neurogenomics

rworkflows:Test, Document, Containerise, and Deploy R Packages

Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers. rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action.

Maintained by Brian Schilder. Last updated 2 months ago.

software workflowmanagement bioconductor containers continuous-integration docker dockerhub github-actions reproducibility workflows

79 stars 7.60 score 6 scripts

ropensci

tic:Tasks Integrating Continuously: CI-Agnostic Workflow Definitions

Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'GitHub Actions' or 'Circle CI'). This package has been peer-reviewed by rOpenSci (v0.3.0.9004).

Maintained by Eli Miller. Last updated 2 months ago.

appveyor continuous-integration deployment githubactions travis-ci

155 stars 7.57 score 16 scripts

kosukeimai

wru:Who are You? Bayesian Prediction of Racial Category Using Surname, First Name, Middle Name, and Geolocation

Predicts individual race/ethnicity using surname, first name, middle name, geolocation, and other attributes, such as gender and age. The method utilizes Bayes' Rule (with optional measurement error correction) to compute the posterior probability of each racial category for any given individual. The package implements methods described in Imai and Khanna (2016) "Improving Ecological Inference by Predicting Individual Ethnicity from Voter Registration Records" Political Analysis <DOI:10.1093/pan/mpw001> and Imai, Olivella, and Rosenman (2022) "Addressing census data problems in race imputation via fully Bayesian Improved Surname Geocoding and name supplements" <DOI:10.1126/sciadv.adc9824>. The package also incorporates the data described in Rosenman, Olivella, and Imai (2023) "Race and ethnicity data for first, middle, and surnames" <DOI:10.1038/s41597-023-02202-2>.

Maintained by Brandon Bertelsen. Last updated 10 months ago.

cpp

133 stars 7.54 score 146 scripts

bcgov

fasstr:Analyze, Summarize, and Visualize Daily Streamflow Data

The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).

Maintained by Jon Goetz. Last updated 6 months ago.

bcgov for frequency-analysis hydat hydrology streamflow summary-statistics trends water

57 stars 7.48 score 89 scripts

molgenis

MolgenisArmadillo:Armadillo Client for the Armadillo Service

A set of functions to manage data shared on a 'MOLGENIS Armadillo' server.

Maintained by Mariska Slofstra. Last updated 1 months ago.

hacktoberfest

3 stars 7.48 score 28 scripts

dyfanjones

noctua:Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)

Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.

Maintained by Dyfan Jones. Last updated 12 months ago.

athena aws database

46 stars 7.48 score 58 scripts

bioc

CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Maintained by Malte Thodberg. Last updated 5 months ago.

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

8 stars 7.46 score 67 scripts 1 dependents

ropensci

allcontributors:Acknowledge all Contributors to a Project

Acknowledge all contributors to a project via a single function call. The function appends to a 'README' or other specified file(s) a table with names of all individuals who contributed via code or repository issues. The package also includes several additional functions to extract and quantify contributions to any repository.

Maintained by Mark Padgham. Last updated 30 days ago.

29 stars 7.46 score 5 scripts 1 dependents

jhudsl

ari:Automated R Instructor

Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.

Maintained by Sean Kross. Last updated 2 years ago.

edtech-software

147 stars 7.43 score 41 scripts 1 dependents

selesnow

rfacebookstat:Load Data from Facebook API Marketing

Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.

Maintained by Alexey Seleznev. Last updated 1 months ago.

31 stars 7.43 score 48 scripts 1 dependents

bioc

glmSparseNet:Network Centrality Metrics for Elastic-Net Regularized Models

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Maintained by André Veríssimo. Last updated 5 months ago.

software statisticalmethod dimensionreduction regression classification survival network graphandnetwork

6 stars 7.42 score 41 scripts 1 dependents

bioc

ELMER:Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Maintained by Tiago Chedraoui Silva. Last updated 5 months ago.

dnamethylation geneexpression motifannotation software generegulation transcription network

7.42 score 176 scripts

ropensci

osmapiR:'OpenStreetMap' API

Interface to 'OpenStreetMap API' for fetching and saving data from/to the 'OpenStreetMap' database (<https://wiki.openstreetmap.org/wiki/API_v0.6>).

Maintained by Joan Maspons. Last updated 4 months ago.

open street map openstreetmap osm openstreetmap-api osmapi api

22 stars 7.42 score 6 scripts

bioc

genefu:Computation of Gene Expression-Based Signatures in Breast Cancer

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Maintained by Benjamin Haibe-Kains. Last updated 4 months ago.

differentialexpression geneexpression visualization clustering classification

7.42 score 193 scripts 3 dependents

bioc

standR:Spatial transcriptome analyses of Nanostring's DSP data in R

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

Maintained by Ning Liu. Last updated 2 months ago.

spatial transcriptomics geneexpression differentialexpression qualitycontrol normalization experimenthubsoftware

18 stars 7.39 score 45 scripts

bioc

cogena:co-expressed gene-set enrichment analysis

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

Maintained by Zhilong Jia. Last updated 5 months ago.

clustering genesetenrichment geneexpression visualization pathways kegg go microarray sequencing systemsbiology datarepresentation dataimport bioconductor bioinformatics

12 stars 7.36 score 32 scripts

bioc

shinyMethyl:Interactive visualization for Illumina methylation arrays

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

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

dnamethylation microarray twochannel preprocessing qualitycontrol methylationarray

5 stars 7.34 score 42 scripts

rundel

ghclass:Tools for Managing Classes on GitHub

Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.

Maintained by Colin Rundel. Last updated 2 months ago.

142 stars 7.32 score 70 scripts

ropensci

riem:Accesses Weather Data from the Iowa Environment Mesonet

Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.

Maintained by Maëlle Salmon. Last updated 1 months ago.

airports asos iowa-environment-mesonet metar peer-reviewed temperature weather weather-api

45 stars 7.30 score 184 scripts

hoxo-m

githubinstall:A Helpful Way to Install R Packages Hosted on GitHub

Provides an helpful way to install packages hosted on GitHub.

Maintained by Koji Makiyama. Last updated 7 years ago.

r-language

49 stars 7.29 score 177 scripts

bioc

OrganismDbi:Software to enable the smooth interfacing of different database packages

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

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

annotation infrastructure

7.26 score 34 scripts 34 dependents

bioc

missMethyl:Analysing Illumina HumanMethylation BeadChip Data

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

Maintained by Belinda Phipson. Last updated 28 days ago.

normalization dnamethylation methylationarray genomicvariation geneticvariability differentialmethylation genesetenrichment

7.24 score 300 scripts 1 dependents

inbo

checklist:A Thorough and Strict Set of Checks for R Packages and Source Code

An opinionated set of rules for R packages and R source code projects.

Maintained by Thierry Onkelinx. Last updated 1 months ago.

checklist continuous-integration continuous-testing quality-assurance

19 stars 7.24 score 21 scripts 2 dependents

hubverse-org

hubUtils:Core 'hubverse' Utilities

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

Maintained by Anna Krystalli. Last updated 19 days ago.

hubverse

6 stars 7.22 score 49 scripts 7 dependents

pik-piam

lucode2:Code Manipulation and Analysis Tools

A collection of tools which allow to manipulate and analyze code.

Maintained by Jan Philipp Dietrich. Last updated 10 days ago.

7.22 score 364 scripts 8 dependents

ropenspain

CatastRo:Interface to the API 'Sede Electronica Del Catastro'

Access public spatial data available under the 'INSPIRE' directive. Tools for downloading references and addresses of properties, as well as map images.

Maintained by Diego Hernangómez. Last updated 7 days ago.

catastro gis maps ropenspain spain spatial static-tiles

23 stars 7.22 score 14 scripts

usaid-oha-si

glamr:SI Utilities Package

Provides a series of base functions useful to the GH OHA SI team. This includes project setup, pulling from DATIM, and key functions for working with the MSD.

Maintained by Aaron Chafetz. Last updated 6 months ago.

2 stars 7.20 score 1.3k scripts 1 dependents

beanumber

etl:Extract-Transform-Load Framework for Medium Data

A predictable and pipeable framework for performing ETL (extract-transform-load) operations on publicly-accessible medium-sized data set. This package sets up the method structure and implements generic functions. Packages that depend on this package download specific data sets from the Internet, clean them up, and import them into a local or remote relational database management system.

Maintained by Benjamin S. Baumer. Last updated 1 years ago.

129 stars 7.17 score 38 scripts 1 dependents

ropensci

bowerbird:Keep a Collection of Sparkly Data Resources

Tools to get and maintain a data repository from third-party data providers.

Maintained by Ben Raymond. Last updated 19 days ago.

ropensci antarctic southern ocean data environmental satellite climate peer-reviewed

50 stars 7.16 score 16 scripts 1 dependents

ropensci

pkgcheck:rOpenSci Package Checks

Check whether a package is ready for submission to rOpenSci's peer review system.

Maintained by Mark Padgham. Last updated 20 days ago.

compliance-automation software-analysis software-checking

19 stars 7.13 score 29 scripts 1 dependents

bioc

ATACseqQC:ATAC-seq Quality Control

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.

Maintained by Jianhong Ou. Last updated 3 months ago.

sequencing dnaseq atacseq generegulation qualitycontrol coverage nucleosomepositioning immunooncology

7.12 score 146 scripts 1 dependents

correlaid

restatis:R Wrapper to Access a Wide Range of Germany's Federal Statistical System Databases Based on the GENESIS Web Service RESTful API of the German Federal Statistical Office (Statistisches Bundesamt/Destatis)

A RESTful API wrapper for accessing the GENESIS database of the German Federal Statistical Office (Destatis) as well as its Census Database and the database of Germany's regional statistics. Supports data search functions, credential management, result caching, and handling remote background jobs for large datasets.

Maintained by Yannik Buhl. Last updated 7 days ago.

22 stars 7.10 score 11 scripts

bioc

RiboCrypt:Interactive visualization in genomics

R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.

Maintained by Michal Swirski. Last updated 3 days ago.

software sequencing riboseq rnaseq

5 stars 7.08 score 22 scripts

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 1 months ago.

8 stars 7.07 score 13 scripts

jamgreen

lehdr:Grab Longitudinal Employer-Household Dynamics (LEHD) Flat Files

Designed to query Longitudinal Employer-Household Dynamics (LEHD) workplace/residential association and origin-destination flat files and optionally aggregate Census block-level data to block group, tract, county, or state. Data comes from the LODES FTP server <https://lehd.ces.census.gov/data/lodes/LODES8/>.

Maintained by Jamaal Green. Last updated 4 months ago.

62 stars 7.05 score 90 scripts

ropensci

mregions2:Access Data from Marineregions.org: Gazetteer & Data Products

Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.

Maintained by Salvador Jesús Fernández Bejarano. Last updated 7 days ago.

9 stars 7.03 score 40 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

77 stars 7.03 score 92 scripts

benrwoodard

adobeanalyticsr:R Client for 'Adobe Analytics' API 2.0

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

Maintained by Ben Woodard. Last updated 2 months ago.

18 stars 7.02 score 39 scripts

permaverse

flipr:Flexible Inference via Permutations in R

A flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing, on any kind of data, be it univariate, multivariate, or more complex such as network-valued data, topological data, functional data or density-valued data.

Maintained by Aymeric Stamm. Last updated 12 days ago.

cpp

6 stars 7.02 score 24 scripts 1 dependents

r-lib

roxygen2md:'Roxygen' to 'Markdown'

Converts elements of 'roxygen' documentation to 'markdown'.

Maintained by Kirill Müller. Last updated 4 months ago.

documentation markdown

68 stars 7.00 score 11 scripts 2 dependents

bioc

mygene:Access MyGene.Info_ services

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.

Maintained by Adam Mark, Cyrus Afrasiabi, Chunlei Wu. Last updated 5 months ago.

annotation

7.00 score 330 scripts 1 dependents

paul-carteron

happign:R Interface to 'IGN' Web Services

Automatic open data acquisition from resources of IGN ('Institut National de Information Geographique et forestiere') (<https://www.ign.fr/>). Available datasets include various types of raster and vector data, such as digital elevation models, state borders, spatial databases, cadastral parcels, and more. There also access to point clouds data ('LIDAR') and specifics API (<https://apicarto.ign.fr/api/doc/>).

Maintained by Paul Carteron. Last updated 3 days ago.

31 stars 6.96 score 35 scripts

thinkr-open

thinkr:Tools for Cleaning Up Messy Files

Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

29 stars 6.96 score 45 scripts

bioc

isobar:Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Maintained by Florian P Breitwieser. Last updated 5 months ago.

immunooncology proteomics massspectrometry bioinformatics multiplecomparisons qualitycontrol

10 stars 6.96 score 19 scripts

bioc

psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.

sequencing rnaseq alternativesplicing differentialsplicing transcription gui principalcomponent survival biomedicalinformatics transcriptomics immunooncology visualization multiplecomparison geneexpression differentialexpression alternative-splicing bioconductor data-analyses differential-gene-expression differential-splicing-analysis gene-expression gtex recount2 rna-seq-data splicing-quantification sra tcga vast-tools cpp

36 stars 6.95 score 31 scripts

sportsdataverse

hoopR:Access Men's Basketball Play by Play Data

A utility to quickly obtain clean and tidy men's basketball play by play data. Provides functions to access live play by play and box score data from ESPN<https://www.espn.com> with shot locations when available. It is also a full NBA Stats API<https://www.nba.com/stats/> wrapper. It is also a scraping and aggregating interface for Ken Pomeroy's men's college basketball statistics website<https://kenpom.com>. It provides users with an active subscription the capability to scrape the website tables and analyze the data for themselves.

Maintained by Saiem Gilani. Last updated 1 years ago.

basketball college-basketball espn kenpom nba nba-analytics nba-api nba-data nba-statistics nba-stats nba-stats-api ncaa ncaa-basketball ncaa-bracket ncaa-players ncaa-ratings ncaam sportsdataverse

91 stars 6.93 score 261 scripts

bioc

pRolocGUI:Interactive visualisation of spatial proteomics data

The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.

Maintained by Lisa Breckels. Last updated 5 months ago.

proteomics visualization gui

8 stars 6.90 score 3 scripts

paws-r

paws.mobile:'Amazon Web Services' Mobile Services

Interface to 'Amazon Web Services' mobile services, including the 'Amplify' library for mobile applications, 'AppSync' back-end for mobile applications, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.media.services:'Amazon Web Services' Media Services Services

Interface to 'Amazon Web Services' media services services, including 'Kinesis' video stream capture and processing, format conversion, and more <https://aws.amazon.com/media-services/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.migration:'Amazon Web Services' Migration & Transfer Services

Interface to 'Amazon Web Services' migration & transfer services, including file and database migration to 'Amazon Web Services' <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.internet.of.things:'Amazon Web Services' Internet of Things Services

Interface to 'Amazon Web Services' internet of things ('IoT') services, including data collection, management, and analysis for IoT devices. <https://aws.amazon.com/iot/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.game.development:'Amazon Web Services' Game Development Services

Interface to 'Amazon Web Services' game development services, including 'GameLift' game server hosting <https://aws.amazon.com/gametech/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.business.applications:'Amazon Web Services' Business Applications Services

Interface to 'Amazon Web Services' business applications services, including online meetings and video conferencing, email and calendar service, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

paws-r

paws.robotics:'Amazon Web Services' Robotics Services

Interface to 'Amazon Web Services' robotics services, including the 'RobotMaker' API for developing, testing, and deploying intelligent robotics applications <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 18 days ago.

aws aws-sdk

332 stars 6.90 score

dfe-analytical-services

dfeR:Common Department for Education Analysis Tasks

Preferred methods for common analytical tasks that are undertaken across the Department, including number formatting, project templates and curated reference data.

Maintained by Cam Race. Last updated 1 months ago.

12 stars 6.89 score 8 scripts

bioc

SomaticSignatures:Somatic Signatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

Maintained by Julian Gehring. Last updated 5 months ago.

sequencing somaticmutation visualization clustering genomicvariation statisticalmethod

22 stars 6.85 score 54 scripts 1 dependents

bioc

RnBeads:RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Maintained by Fabian Mueller. Last updated 2 months ago.

dnamethylation methylationarray methylseq epigenetics qualitycontrol preprocessing batcheffect differentialmethylation sequencing cpgisland immunooncology twochannel dataimport

6.85 score 169 scripts 1 dependents

pik-piam

edgeTransport:Prepare EDGE Transport Data for the REMIND model

EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation with a high level of detail in its representation of technological and modal options. It is a partial equilibrium model with a nested multinomial logit structure and relies on the modified logit formulation. Most of the sources are not publicly available. PIK-internal users can find the sources in the distributed file system in the folder `/p/projects/rd3mod/inputdata/sources/EDGE-Transport-Standalone`.

Maintained by Johanna Hoppe. Last updated 2 days ago.

5 stars 6.84 score 16 scripts 2 dependents

raymondbalise

rUM:R Templates from the University of Miami

This holds some r markdown and quarto templates and a template to create a research project in "R Studio".

Maintained by Raymond Balise. Last updated 10 days ago.

rmarkdown

9 stars 6.84 score 16 scripts

ready4-dev

ready4:Develop and Use Modular Health Economic Models

A template model module, tools to help find model modules derived from this template and a programming syntax to use these modules in health economic analyses. These elements are the foundation for a prototype software framework for developing living and transferable models and using those models in reproducible health economic analyses. The software framework is extended by other R libraries. For detailed documentation about the framework and how to use it visit <https://www.ready4-dev.com/>. For a background to the methodological issues that the framework is attempting to help solve, see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.

Maintained by Matthew Hamilton. Last updated 5 months ago.

computational-modeling health-economics software-framework

2 stars 6.84 score 95 scripts

yonicd

carbonate:Interact with 'carbon.js'

Create beautiful images of source code using 'carbon.js'<https://carbon.now.sh/about>.

Maintained by Jonathan Sidi. Last updated 3 years ago.

212 stars 6.83 score 32 scripts

kozodoi

fairness:Algorithmic Fairness Metrics

Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.

Maintained by Nikita Kozodoi. Last updated 2 years ago.

algorithmic-discrimination algorithmic-fairness discrimination disparate-impact fairness fairness-ai fairness-ml machine-learning

32 stars 6.82 score 69 scripts 1 dependents

emilyriederer

projmgr:Task Tracking and Project Management with GitHub

Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.

Maintained by Emily Riederer. Last updated 1 years ago.

github-api project-management

124 stars 6.81 score 34 scripts 5 dependents

r-arcgis

arcgisgeocode:A Robust Interface to ArcGIS 'Geocoding Services'

A very fast and robust interface to ArcGIS 'Geocoding Services'. Provides capabilities for reverse geocoding, finding address candidates, character-by-character search autosuggestion, and batch geocoding. The public 'ArcGIS World Geocoder' is accessible for free use via 'arcgisgeocode' for all services except batch geocoding. 'arcgisgeocode' also integrates with 'arcgisutils' to provide access to custom locators or private 'ArcGIS World Geocoder' hosted on 'ArcGIS Enterprise'. Learn more in the 'Geocode service' API reference <https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.

Maintained by Josiah Parry. Last updated 2 months ago.

rust cargo

42 stars 6.81 score 20 scripts 1 dependents

bioc

ideal:Interactive Differential Expression AnaLysis

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

Maintained by Federico Marini. Last updated 3 months ago.

immunooncology geneexpression differentialexpression rnaseq sequencing visualization qualitycontrol gui genesetenrichment reportwriting shinyapps bioconductor differential-expression reproducible-research rna-seq rna-seq-analysis shiny user-friendly

29 stars 6.78 score 5 scripts

ixpantia

tapLock:Seamless Single Sign-on for 'shiny'

Swift and seamless Single Sign-On (SSO) integration. Designed for effortless compatibility with popular Single Sign-On providers like Google and Microsoft, it streamlines authentication, enhancing both user experience and application security. Elevate your 'shiny' applications for a simplified, unified, and secure authentication process.

Maintained by Andres Quintero. Last updated 5 months ago.

prodverse

30 stars 6.78 score 10 scripts