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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software resource, software toolkit | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-09-12 01:02:23 | 0 | ||||||
|
ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/, https://sources.debian.org/src/r-cran-adegenet/ | SCR_000825 | R/ADEGENET | 2026-09-12 01:02:24 | 22 | |||||
|
brms Resource Report Resource Website 1+ mentions |
brms (RRID:SCR_023862) | software resource, software toolkit | Software package implements Bayesian multilevel models in R using probabilistic programming language Stan. | Bayesian multilevel models, R, probabilistic programming language Stan, | is listed by: CRAN | DOI:10.18637/jss.v080.i01 | Free, Available for download, Freely available | SCR_023862 | 2026-09-12 01:03:06 | 7 | |||||||||
|
lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | software resource, source code | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-09-12 01:03:58 | 411 | |||||||
|
WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | R/WEIGHTED_FDR | 2026-09-12 01:02:49 | 0 | ||||||||
|
imDEV Resource Report Resource Website 1+ mentions |
imDEV (RRID:SCR_014674) | software application, software resource, systems interoperability software | A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data. | statistical analysis, statistical analysis package, r, r package, excel, data visualization, feature selection, omics, systems interoperability, software, metabolomics, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/bts439 | Supports Microsoft Excel versions 2003-2010 | biotools:imdev | https://sourceforge.net/projects/imdev/, https://bio.tools/imdev | SCR_014674 | Interactive modules for Data Exploration and Visualization, Interactive modules for Data Exploration and Visualization (imDEV) | 2026-09-12 01:02:51 | 8 | ||||||
|
devtools Resource Report Resource Website 10+ mentions |
devtools (RRID:SCR_016961) | software resource, software toolkit | Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks. | make, developing, R, package, easier |
is used by: riboWaltz is used by: dndSCV is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016961 | 2026-09-12 01:02:54 | 20 | ||||||||||
|
viridis Resource Report Resource Website 10+ mentions |
viridis (RRID:SCR_016696) | software resource, software toolkit | Software package which brings to R color scales. Created for the Python matplotlib library. | R, color, scale, Python, matplotlib, CRAN |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://github.com/sjmgarnier/viridis | SCR_016696 | 2026-09-12 01:02:54 | 30 | |||||||||
|
MAREYMAP Resource Report Resource Website 10+ mentions |
MAREYMAP (RRID:SCR_009066) | MAREYMAP | software application, software resource | Software application that is a meiotic recombination rate estimation program. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, tcl/tk | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154056 | SCR_009066 | 2026-09-12 01:02:39 | 41 | ||||||||
|
TRAP Resource Report Resource Website 100+ mentions |
TRAP (RRID:SCR_009002) | TRAP | software application, software resource | Software tool for determining a regression model of quantitative or binary trait variation when the number of possible genetic predictors is very large, considering only a moderate number of predictors at one time, using unrelated or family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, any with r installation | is listed by: Genetic Analysis Software | nlx_154010 | SCR_009002 | Tiled Regression Analysis Package | 2026-09-12 01:02:38 | 397 | ||||||||
|
SIMULAPLOT Resource Report Resource Website |
SIMULAPLOT (RRID:SCR_009079) | SIMULAPLOT | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models. | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154089 | http://www.chg.duke.edu/research/simlaplot.html | SCR_009079 | 2026-09-12 01:02:39 | 0 | |||||||
|
CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software application, software resource | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | Case-Control association analysis with RELlated individuals | 2026-09-12 01:02:40 | 0 | |||||||
|
PEER Resource Report Resource Website 500+ mentions |
PEER (RRID:SCR_009326) | PEER | software application, software resource | Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python. | gene, genetic, genomic, c++, r, python |
is listed by: Genetic Analysis Software is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21283789 PMID:20463871 |
nlx_154532, OMICS_04597 | https://github.com/PMBio/peer/wiki | SCR_009326 | 2026-09-12 01:02:44 | 579 | |||||||
|
PEDVIZAPI Resource Report Resource Website |
PEDVIZAPI (RRID:SCR_009325) | PEDVIZAPI | software application, software resource | A Java Api for the visual analysis of large and complex pedigrees that provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, r | is listed by: Genetic Analysis Software | nlx_154531 | SCR_009325 | PEDigree VIsualiZation API | 2026-09-12 01:02:44 | 0 | ||||||||
|
R/SNP.PLOTTER Resource Report Resource Website 1+ mentions |
R/SNP.PLOTTER (RRID:SCR_009376) | software application, software resource | An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154599, SCR_009405, nlx_154649 | https://github.com/cannin/snp_plotter | http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html | SCR_009376 | SNP.PLOTTER | 2026-09-12 01:02:45 | 2 | |||||||
|
R/METASIM Resource Report Resource Website 1+ mentions |
R/METASIM (RRID:SCR_009370) | software application, software resource | An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, c++, unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154592 | http://linum.cofc.edu/software.html | SCR_009370 | METApopulation SIMulation | 2026-09-12 01:02:45 | 1 | ||||||||
|
ROMPREV Resource Report Resource Website |
ROMPREV (RRID:SCR_009361) | ROMPREV | software application, software resource | Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, any with r installation, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154577, biotools:romprev | https://bio.tools/romprev | SCR_009361 | Regression of Offspring on Mid-Parent (REVised) | 2026-09-12 01:02:45 | 0 | |||||||
|
GC/GCF Resource Report Resource Website 1+ mentions |
GC/GCF (RRID:SCR_009075) | software application, software resource | Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, linux | is listed by: Genetic Analysis Software | SCR_000846, nlx_154072, nlx_154584 | SCR_009075 | R/GCF, R/GC, Genomic Control | 2026-09-12 01:02:02 | 1 | |||||||||
|
COVIBD Resource Report Resource Website |
COVIBD (RRID:SCR_009155) | software application, software resource | Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154207, SCR_009109, nlx_154275 | SCR_009155 | R/COVIBD | 2026-09-12 01:02:02 | 0 | |||||||||
|
tsne Resource Report Resource Website 1+ mentions |
tsne (RRID:SCR_024305) | software resource, software toolkit | Softare R package as implementation of the t-SNE algorithm. | t-SNE algorithm implementation, R | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-tsne/ | SCR_024305 | 2026-09-12 01:01:17 | 6 |
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