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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-19 12:58:05 | 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 | 2026-09-19 12:58:05 | 1 | ||||||||
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R/HAPASSOC Resource Report Resource Website |
R/HAPASSOC (RRID:SCR_009365) | software application, software resource | Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154587, SCR_009219, nlx_154374 | http://stat-db.stat.sfu.ca:8080/statgen/research/hapassoc | SCR_009365 | HAPASSOC | 2026-09-19 12:58:05 | 0 | ||||||||
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SIMULA Resource Report Resource Website 1+ mentions |
SIMULA (RRID:SCR_009390) | SIMULA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members. | gene, genetic, genomic, java, r, unix, solaris, linux, ms-windows |
is listed by: Genetic Analysis Software is related to: DE-Sim |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154629 | http://www.chg.duke.edu/research/simla30.html | SCR_009390 | 2026-09-19 12:58:06 | 1 | |||||||
|
TAGSTER Resource Report Resource Website 1+ mentions |
TAGSTER (RRID:SCR_009413) | software application, software resource | Software tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, r, linux, macos, ms-windows | is listed by: Genetic Analysis Software | nlx_154673 | SCR_009413 | 2026-09-19 12:58:06 | 2 | ||||||||||
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R/QTLDESIGN Resource Report Resource Website 1+ mentions |
R/QTLDESIGN (RRID:SCR_013424) | software application, software resource | Software application to help plan quantitative trait locus (QTL) experiments. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154598 | https://cran.r-project.org/web/packages/qtlDesign/index.html | SCR_013424 | 2026-09-19 12:58:10 | 9 | |||||||||
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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 | 2026-09-19 12:58:13 | 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 | 2026-09-19 12:58:12 | 3080 | ||||||||
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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 | 2026-09-19 12:58:19 | 8 | |||||||||
|
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 | 2026-09-19 12:58:21 | 44 | |||||||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-09-19 12:58:33 | 35 | ||||||
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R-package for adaptive fMRI analysis Resource Report Resource Website |
R-package for adaptive fMRI analysis (RRID:SCR_002530) | R-package for adaptive fMRI analysis | data processing software, image analysis software, image processing software, software application, software resource | The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155935 | SCR_002530 | 2026-09-19 12:55:05 | 0 | ||||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-19 12:55:09 | 1104 | |||||
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iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-19 12:55:28 | 0 | ||||||
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LDHEATMAP Resource Report Resource Website 100+ mentions |
LDHEATMAP (RRID:SCR_006312) | software application, software resource | Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154424, SCR_009347, nlx_154561 | http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap | SCR_006312 | R/LDHEATMAP | 2026-09-19 12:55:55 | 169 | ||||||||
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HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | R/HCLUST | 2026-09-19 12:55:59 | 1460 | ||||||
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survminer Resource Report Resource Website 100+ mentions |
survminer (RRID:SCR_021094) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package provides functions for facilitating survival analysis and visualization. | survival analysis, survival visualization, R | is related to: R Project for Statistical Computing | Free, Available for download, Freely available | SCR_021094 | 2026-09-19 12:54:48 | 133 | ||||||||||
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rstatix Resource Report Resource Website 100+ mentions |
rstatix (RRID:SCR_021240) | data analytics software, software application, software resource, software toolkit | Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances. | Statistical tests, t-test, Wilcoxon test, ANOVA, Kruskal-Wallis, correlation analyses, R, visualization | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/kassambara/rstatix | SCR_021240 | 2026-09-19 12:54:50 | 133 | |||||||||
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scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-09-19 12:53:15 | 187 | ||||||
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jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | data analysis software, data processing software, software application, software resource | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-09-19 12:53:18 | 4164 |
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