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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SWEEP Resource Report Resource Website 10+ mentions |
SWEEP (RRID:SCR_009418) | SWEEP | software resource, software application | Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:sweep, nlx_154667 | https://bio.tools/sweep | SCR_009418 | 2026-08-07 09:27:05 | 32 | ||||||||
|
SUMSTAT Resource Report Resource Website 10+ mentions |
SUMSTAT (RRID:SCR_009416) | software resource, software application | Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, free pascal, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154663, biotools:sumstat | https://bio.tools/sumstat | SCR_009416 | 2026-08-07 09:26:58 | 11 | |||||||||
|
SUP Resource Report Resource Website |
SUP (RRID:SCR_009417) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software. | gene, genetic, genomic, c, c++, unix, linux, cygwin, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is related to: SLINK is related to: FASTSLINK is related to: bio.tools |
PMID:16803631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154664, biotools:sup | https://bio.tools/sup | SCR_009417 | Slink Utility Program | 2026-08-07 09:27:02 | 0 | ||||||
|
SNPTEST Resource Report Resource Website 100+ mentions |
SNPTEST (RRID:SCR_009406) | software resource, software application | Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154651, biotools:snptest | https://bio.tools/snptest | http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html | SCR_009406 | 2026-08-07 09:26:58 | 401 | ||||||||
|
SKAT Resource Report Resource Website 100+ mentions |
SKAT (RRID:SCR_009396) | software resource, software application | Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154634, biotools:skat | https://bio.tools/skat | SCR_009396 | SNP-set (Sequence) Kernel Association Test | 2026-08-07 09:26:57 | 287 | ||||||||
|
SIMPED Resource Report Resource Website 1+ mentions |
SIMPED (RRID:SCR_009388) | software resource, software application | Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-window, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:simped, nlx_154627 | https://bio.tools/simped | http://www.hgsc.bcm.tmc.edu/genemapping | SCR_009388 | 2026-08-07 09:27:01 | 1 | ||||||||
|
SIBLINK Resource Report Resource Website |
SIBLINK (RRID:SCR_009381) | software resource, software application | Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:siblink, nlx_154616 | https://bio.tools/siblink | http://wwwchg.duhs.duke.edu/software/siblink.html | SCR_009381 | 2026-08-07 09:26:57 | 0 | ||||||||
|
PRESTO: Genetic Association Analysis Software Resource Report Resource Website 1+ mentions |
PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) | software resource, software application | Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data. | gene, genetic, genomic, java, ms-windows, unix, solaris, linux, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu138 | nlx_154549 | SCR_013285 | 2026-08-07 09:27:46 | 2 | |||||||||
|
mothur Resource Report Resource Website 5000+ mentions |
mothur (RRID:SCR_011947) | standalone software, software resource, software application | An open-source software package for describing and comparing microbial communities. It incorporates the functionality of a number of computational tools, calculators, and visualization tools. | microbiome, microbial ecology, open source, bioinformatics, standalone software |
is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian |
DOI:10.1128/AEM.01541-09 | Open source | OMICS_01518 | https://github.com/mothur/mothur/releases/tag/v1.38.1.1, https://sources.debian.org/src/mothur/ | SCR_011947 | 2026-08-07 09:27:29 | 6270 | |||||||
|
THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software resource, software application | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-08-07 09:27:53 | 53 | |||||
|
VISTA Browser Resource Report Resource Website 100+ mentions |
VISTA Browser (RRID:SCR_011808) | software resource, software toolkit | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-08-07 09:27:28 | 125 | |||||
|
SASGENE Resource Report Resource Website |
SASGENE (RRID:SCR_013084) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, 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:sasgene, nlx_154608 | https://bio.tools/sasgene | SCR_013084 | 2026-08-07 09:27:44 | 0 | ||||||||
|
TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software resource, software application | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/, https://bio.tools/tassel | SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-08-07 09:27:43 | 2476 | |||||||
|
ECLIPSE Resource Report Resource Website 100+ mentions |
ECLIPSE (RRID:SCR_013130) | software resource, software application | A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, tested on, unix, (compaq tru64 v5.0a), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154290, biotools:eclipse | https://bio.tools/eclipse | SCR_013130 | Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA | 2026-08-07 09:27:51 | 124 | ||||||||
|
SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software resource, software application | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-08-07 09:27:47 | 0 | |||||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | web application, software resource, source code | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml, https://sources.debian.org/src/phyml/ | SCR_014629 | 2026-08-07 09:28:04 | 7951 | |||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | software resource, data analytics software, software application | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-08-07 09:28:08 | 16 | |||||
|
FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | software resource, standalone software, data analytics software, software application | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | 2026-08-07 09:28:06 | 431 | |||||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | software resource, data access protocol | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-08-07 09:28:07 | 3714 | ||||||
|
GNU Octave Resource Report Resource Website 100+ mentions |
GNU Octave (RRID:SCR_014398) | software resource, programming language | A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | command-line, free software, array programming, programming language, mathematics, reproducible research, |
is listed by: Debian is related to: Mastrave modelling library works with: CoSMoMVPA works with: Empirical Gramian Framework |
DOI:10.1016/j.jprocont.2012.04.006 | THIS RESOURCE IS NO LONGER IN SERVICE | https://directory.fsf.org/wiki/Octave, https://sources.debian.org/src/octave/ | SCR_014398 | Octave | 2026-08-07 09:28:06 | 247 |
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