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https://github.com/stanstrup/mwtabR

An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists.

Proper citation: mwtabR (RRID:SCR_014677) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://decipher.cee.wisc.edu/index.html

A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Database Enabled Code for Ideal Probe Hybridization Employing R (RRID:SCR_000581) Copy   

•   Source: SciCrunch Registry

http://www.rstudio.com/shiny/

Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.

Proper citation: Shiny (RRID:SCR_001626) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/

Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

Proper citation: CRAN (RRID:SCR_003005) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/%7Emarchini/software.html

An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)

Proper citation: POPGEN (RRID:SCR_007315) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/psy/index.html

Software package implementing various statistical procedures used in psychometry.

Proper citation: R package: psy (RRID:SCR_015660) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/rentrez/index.html

Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.

Proper citation: rentrez (RRID:SCR_021062) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=car

Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression.

Proper citation: Companion to Applied Regression (RRID:SCR_022137) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/Exact/index.html

Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)

Proper citation: SNP-HWE (RRID:SCR_008555) Copy   

•   Source: SciCrunch Registry

http://www.modelmakertools.com/modelmaker/index.html

Multi-threaded, parallel and CUDA based application that provides an interface to the R statistical language, MATLAB, Accord and Aforge APIs, along with Neural Maestro to accomplish fMRI, EEG, speech signals, commodity price analysis, general machine learning, classification and time series analysis and forecasting. Because it unifies research development work in MATLAB, R and C++, it provides a mathematical canvas the permits researches to experiment with both pure and hybrid models that use the best of all software development languages.

Proper citation: ModelMaker (RRID:SCR_009024) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/meta/index.html

Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software)

Proper citation: R/META (RRID:SCR_009175) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/amelia/

Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)

Proper citation: AMELIA (RRID:SCR_009119) Copy   

•   Source: SciCrunch Registry

http://gump.qimr.edu.au/GAIA/gaia.html

Web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAIA (RRID:SCR_009182) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/ariel/

Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)

Proper citation: ARIEL (RRID:SCR_009126) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~marchini/software.html

A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)

Proper citation: GWAPOWER (RRID:SCR_009216) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/onemap/index.html

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

•   Source: SciCrunch Registry

http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm

An integrated software package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates (entry from Genetic Analysis Software)

Proper citation: R/GAP (RRID:SCR_009364) Copy   

•   Source: SciCrunch Registry