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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mwtabR Resource Report Resource Website |
mwtabR (RRID:SCR_014677) | software resource, source code | An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists. | statistical analysis, statistical analysis package, r, r package, metabolomics, parse | is listed by: Metabolomics Workbench | SCR_014677 | R Package for downloading and parsing mwTab files from the Metabolomics Workbench | 2026-09-05 06:33:59 | 0 | ||||||||||
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ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-05 06:32:20 | 0 | ||||||
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Database Enabled Code for Ideal Probe Hybridization Employing R Resource Report Resource Website 1+ mentions |
Database Enabled Code for Ideal Probe Hybridization Employing R (RRID:SCR_000581) | DECIPHER | software resource, software toolkit | 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. | 16s rrna sequence, chimera, primer, probe, array, 16s oligo, dna sequence, r |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:22101057 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01114 | SCR_000581 | 2026-09-05 06:32:21 | 2 | |||||||
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Shiny Resource Report Resource Website 500+ mentions |
Shiny (RRID:SCR_001626) | software resource, software toolkit | 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. | R, analysis, interactive, web, application |
uses: shinythemes is used by: ClustVis is used by: shinyGEO is used by: PlotsOfData is used by: shinyCircoss is used by: AlloMate is used by: VenomView is used by: bulkAnalyseR is related to: rSPRITE is related to: EHRtemporalVariability is related to: robvis is related to: Omics Data Paper Generator is related to: Mitochondrial Neuron Ubiquitin is related to: chevreul is related to: Click-qPCR is related to: EMImR is related to: Mona has parent organization: RStudio works with: BoxPlotR works with: shinyhelper works with: ShinyCell works with: Breedverse works with: GenoBrew |
PMID:34642739 PMID:26225240 |
Free, Available for download, Freely available | nlx_153894 | SCR_001626 | 2026-09-05 06:32:24 | 590 | ||||||||
|
CAROL Resource Report Resource Website 10+ mentions |
CAROL (RRID:SCR_001800) | CAROL | software application, software resource | 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. | gene, genetic, genomic, r, prediction, non-synonymous coding variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22261837 | Free, Available for download, Freely available | nlx_154254, OMICS_00143 | http://www.sanger.ac.uk/resources/software/carol/ | SCR_001800 | Combined Annotation scoRing toOL | 2026-09-05 06:32:25 | 11 | |||||
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CRAN Resource Report Resource Website 5000+ mentions |
CRAN (RRID:SCR_003005) | CRAN | software repository, software resource | 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. | network, ftp, web, server, code, documentation, mirror, R |
lists: lme4 lists: R package: nlme lists: R package: lmerTest lists: R package: RVAideMemoire lists: R package: LMERConvenienceFunctions lists: R package: psy lists: R package: lattice lists: geomorph lists: Sequenza lists: NeuroAnatomy Toolbox lists: dplyr lists: Prophet lists: metagear lists: tidyr lists: Mediation Analysis of Causality under Confounding lists: MIIVsem lists: rjags lists: GENEPOP lists: webchem lists: cowplot lists: readxl lists: biomod2 lists: multcomp lists: knitr lists: ggtree lists: Minimum-Hypergeometric Test lists: meta lists: Network-Based R-Statistics lists: pavo lists: Modern Applied Statistics with S lists: cvequality lists: openxlsx lists: tidyverse lists: Genomic Annotation in Livestock for positional candidate LOci lists: igraph lists: SIMR lists: gbs2ploidy lists: vioplot lists: spdep lists: maps lists: Differential Gene Correlation Analysis lists: ez lists: celltrackR lists: rentrez lists: pepr lists: survival lists: ggpubr lists: Signac lists: rstatix lists: ggalluvial lists: purrr lists: gtsummary lists: questionr lists: powereQTL lists: RSurveillance lists: epiR lists: psych lists: CCP lists: yacca lists: DHARMa lists: Companion to Applied Regression lists: Peptides lists: taxize lists: seqinr lists: reshape2 lists: mvabund lists: CpGassoc lists: metaMA lists: ComplexUpset lists: eulerr lists: shinyhelper lists: shinythemes lists: philentropy lists: lwgeom lists: stringr lists: ordinal lists: msigdbr lists: meta4diag lists: Rtrack lists: ggsignif lists: Corrplot lists: immunarch lists: Algorithms and Framework for Nonnegative Matrix Factorization lists: Computing Chance Corrected Agreement Coefficients lists: Intraclass Correlations for Quantifying Inter Rater Reliability lists: Regression Modeling Strategies lists: caret lists: AICcmodavg lists: RHRV lists: FFTrees lists: Simple Features lists: rworldmap lists: eHDprep lists: vcfR lists: vtree lists: SimplyAgree lists: randomizeR lists: DiagrammeR lists: forestplot lists: merTools lists: clusterSim lists: bibliometrix lists: Rtsne lists: brms lists: oncoPredict lists: epitools lists: DrugSim2DR lists: rstanarm lists: scCustomize lists: corrplot lists: Parsnip lists: ggbreak lists: FactoMineR lists: tidycmprsk lists: BioCircos lists: Matrix based Flexible Project Planning is affiliated with: R Project for Statistical Computing is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is affiliated with: ANOCVA is related to: flowBin is related to: CorMut is related to: VariantAnnotation is related to: timecourse is related to: RmiR.Hs.miRNA is related to: PSCBS is related to: sybil - Efficient Constrained Based Modelling in R is related to: categoryCompare is related to: clValid is related to: pheatmap is related to: RaceID is related to: BRASS is related to: IDR is related to: ascend is related to: brainGraph is related to: GBM R package is related to: Phangorn is related to: ape is related to: missForest is related to: trend is related to: precrec is related to: EHRtemporalVariability is related to: emmeans is related to: reshape is related to: variancePartition is related to: SimFFPE is related to: FilterFFPE is related to: shinyCircoss is related to: Betareg is related to: ggeffects is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: ggforce is related to: janitor is related to: Rphenograph is parent organization of: Postgwas is parent organization of: MetaDE is parent organization of: MCMC.qpcr is parent organization of: PurBayes is parent organization of: circlize is parent organization of: neuRosim is parent organization of: metaRNASeq is parent organization of: RankAggreg is parent organization of: DEMI is parent organization of: Iterative Signature Algorithm is parent organization of: MUMA is parent organization of: VennDiagram is parent organization of: ExomeDepth is parent organization of: FisHiCal is parent organization of: CNVassoc is parent organization of: aCGH.Spline is parent organization of: Isopat is parent organization of: enviPat is parent organization of: Parametric Time Warping is parent organization of: enviPick is parent organization of: pairheatmap is parent organization of: RCircos is parent organization of: MultiPhen is parent organization of: aLFQ is parent organization of: MetaQC is parent organization of: YuGene is parent organization of: Kdetrees is parent organization of: ggplot2 is parent organization of: R package inTrees is parent organization of: ggrepel hosts: MSM |
nif-0000-30270 | http://cran.r-project.org/mirrors.html | SCR_003005 | the Comprehensive R Archive Network, Comprehensive R Archive Network, The Comprehensive R Archive Network | 2026-09-05 06:32:28 | 7039 | |||||||
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POPGEN Resource Report Resource Website 100+ mentions |
POPGEN (RRID:SCR_007315) | software application, software resource | 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) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154543, SCR_009374, nlx_154596 | http://mathgen.stats.ox.ac.uk/software.html, https://cran.r-project.org/web/packages/popgen/index.html | SCR_007315 | R/POPGEN | 2026-09-05 06:32:38 | 205 | ||||||||
|
R package: psy Resource Report Resource Website 1+ mentions |
R package: psy (RRID:SCR_015660) | software resource, software toolkit | Software package implementing various statistical procedures used in psychometry. | r, r package, psychometry, statistical analysis | is listed by: CRAN | Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015660 | Package ‘psy’, psy: Various procedures used in psychometry, psy | 2026-09-05 06:33:00 | 1 | |||||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | 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. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-09-05 06:32:59 | 3080 | ||||||||
|
rentrez Resource Report Resource Website 1+ mentions |
rentrez (RRID:SCR_021062) | software resource, software toolkit | 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. | R, entrez, function, NCBI Eutils API, search databases, interact with NCBI databases |
is listed by: CRAN works with: GenBank works with: PubMed |
Free, Available for download, Freely available | https://github.com/ropensci/rentrez/ | SCR_021062 | 2026-09-05 06:33:06 | 8 | |||||||||
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Companion to Applied Regression Resource Report Resource Website 10+ mentions |
Companion to Applied Regression (RRID:SCR_022137) | car | software resource, software toolkit | Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression. | R, companion to applied regression | is listed by: CRAN | Free, Available for download, Freely available | SCR_022137 | 2026-09-05 06:33:09 | 44 | |||||||||
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SNP-HWE Resource Report Resource Website 1+ mentions |
SNP-HWE (RRID:SCR_008555) | SNP-HWE | software application, software resource | Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, c, c++, r | is listed by: Genetic Analysis Software | nlx_154645 | SCR_008555 | 2026-09-05 06:32:40 | 4 | |||||||||
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ModelMaker Resource Report Resource Website 10+ mentions |
ModelMaker (RRID:SCR_009024) | ModelMaker | software application, software resource | 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. | fmri, eeg, speech signal, commodity price analysis, machine learning, classification, time series analysis, forecasting, time series, r, matlab |
is related to: iBIOFind is related to: Neural Maestro has parent organization: The Cromwell Workshop |
Request required | nlx_153828 | http://neuronalarchitects.com/model-maker.html | SCR_009024 | Model Maker | 2026-09-05 06:32:41 | 17 | ||||||
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R/META Resource Report Resource Website 50+ mentions |
R/META (RRID:SCR_009175) | R/META | software application, software resource | Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154307 | SCR_009175 | 2026-09-05 06:32:45 | 65 | |||||||||
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AMELIA Resource Report Resource Website 100+ mentions |
AMELIA (RRID:SCR_009119) | AMELIA | software application, software resource | 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) | gene, genetic, genomic, r, unix, linux | is listed by: Genetic Analysis Software | nlx_154222 | SCR_009119 | Allele Matching Empirical Locus-specific Integrated Association test | 2026-09-05 06:32:44 | 127 | ||||||||
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GAIA Resource Report Resource Website 100+ mentions |
GAIA (RRID:SCR_009182) | GAIA | software application, software resource | 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. | gene, genetic, genomic, perl, r, web-based | is listed by: Genetic Analysis Software | DOI:10.1186/1471-2350-7-34 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154320 | http://www.bbu.cf.ac.uk/html/research/biostats.htm | SCR_009182 | Genetic Association Interaction Analysis | 2026-09-05 06:32:46 | 182 | |||||
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ARIEL Resource Report Resource Website 10+ mentions |
ARIEL (RRID:SCR_009126) | ARIEL | software application, software resource | 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) | gene, genetic, genomic, r, unix, linux | is listed by: Genetic Analysis Software | nlx_154231 | SCR_009126 | Accumulation of Rare variants Integrated and Extended Locus-specific test | 2026-09-05 06:32:44 | 48 | ||||||||
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GWAPOWER Resource Report Resource Website 1+ mentions |
GWAPOWER (RRID:SCR_009216) | software application, software resource | 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) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154369, nlx_154586, SCR_000847 | SCR_009216 | R/GWAPOWER, Genome-Wide Association POWER | 2026-09-05 06:32:47 | 8 | |||||||||
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R/ONEMAP Resource Report Resource Website 10+ mentions |
R/ONEMAP (RRID:SCR_009371) | software application, software resource | 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) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154502, SCR_009312, nlx_154593 | http://www.ciagri.usp.br/~aafgarci/OneMap/ | SCR_009371 | ONEMAP | 2026-09-05 06:32:51 | 22 | ||||||||
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R/GAP Resource Report Resource Website 1+ mentions |
R/GAP (RRID:SCR_009364) | R/GAP | software application, software resource | 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) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154583 | SCR_009364 | R/Genetic Analysis Package | 2026-09-05 06:32:51 | 1 |
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