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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TRAP Resource Report Resource Website 100+ mentions |
TRAP (RRID:SCR_009002) | TRAP | software resource, software application | 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 | 2026-02-14 02:07:11 | 394 | ||||||||
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2SNP Resource Report Resource Website 1+ mentions |
2SNP (RRID:SCR_009038) | 2SNP | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals. | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:18451440 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154003 | https://omictools.com/2snp-tool | http://alla.cs.gsu.edu/~software/2SNP/ | SCR_009038 | 2026-02-14 02:06:43 | 2 | |||||
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AGEINF Resource Report Resource Website |
AGEINF (RRID:SCR_009039) | AGEINF | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation. | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | Aging | PMID:10978301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154004 | http://www.math.sfu.ca/~jgraham/Papers/Programs/AgeCode/ | SCR_009039 | 2026-02-14 02:07:06 | 0 | |||||
|
ALBERT Resource Report Resource Website 10+ mentions |
ALBERT (RRID:SCR_009037) | ALBERT | software resource, software application | Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:albert, nlx_154002 | https://bio.tools/albert | SCR_009037 | A Likelihood Based Estimation of Risk in Trios | 2026-02-14 02:07:11 | 47 | |||||||
|
ACT Resource Report Resource Website |
ACT (RRID:SCR_009033) | ACT | software resource, software application | Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77, c++, unix, solaris 2.4 | is listed by: Genetic Analysis Software | nlx_153997 | http://www.epigenetic.org/Linkage/act.tar.gz | SCR_009033 | Analysis of Complex Traits | 2026-02-14 02:06:43 | 0 | |||||||
|
SNPHAP Resource Report Resource Website 10+ mentions |
SNPHAP (RRID:SCR_008456) | SNPHAP | software resource, software application | Software program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects (entry from Genetic Analysis Software) | gene, genetic, genomic, c, c++ | is listed by: Genetic Analysis Software | nlx_154642 | SCR_008456 | 2026-02-14 02:06:42 | 30 | |||||||||
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SIMCOAL Resource Report Resource Website 1+ mentions |
SIMCOAL (RRID:SCR_008450) | SIMCOAL | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, (9x/nt) | is listed by: Genetic Analysis Software | nlx_154620 | SCR_008450 | SIMulate COAlescence | 2026-02-14 02:06:54 | 8 | ||||||||
|
FASTLINK Resource Report Resource Website 50+ mentions |
FASTLINK (RRID:SCR_009177) | FASTLINK | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, vms, ms-dos, .. and can also run in parallel on shared memory unix machines |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:8807326 | OMICS_28405, nlx_154309 | https://sources.debian.org/src/fastlink/ | SCR_009177 | faster version of LINKAGE LINKAGE | 2026-02-14 02:06:46 | 58 | ||||||
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FASTEHPLUS Resource Report Resource Website |
FASTEHPLUS (RRID:SCR_009176) | FASTEHPLUS | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 7, 2016. | gene, genetic, genomic, c, ms-windows, unix, dec, osf, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154308 | http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/ | SCR_009176 | EHPLUS, faster EH-PLUS EH | 2026-02-14 02:07:14 | 0 | ||||||
|
ERPA Resource Report Resource Website 1+ mentions |
ERPA (RRID:SCR_009173) | ERPA | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for non-parametric analysis (entry from Genetic Analysis Software) | gene, genetic, genomic, c, ms-dos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154302 | SCR_009173 | Extended Relative Pair Analysis | 2026-02-14 02:06:46 | 7 | |||||||
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EXOMEPICKS Resource Report Resource Website 1+ mentions |
EXOMEPICKS (RRID:SCR_009174) | EXOMEPICKS | software resource, software application | Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (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_154306, biotools:exomepicks | https://bio.tools/exomepicks | SCR_009174 | 2026-02-14 02:07:09 | 6 | ||||||||
|
EMLD Resource Report Resource Website 1+ mentions |
EMLD (RRID:SCR_009171) | EMLD | software resource, software application | Software application to calculate pair-wise linkage disequilibrium based on SNP genotype data from unrelated individuals. EM algorithm is used to estimate pair-wise haplotype frequencies. The output file is in the format of input file for GOLD program, thus it can be directly plug into GOLD to get LD plots. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154298 | http://epi.mdanderson.org/~qhuang/Software/pub.htm | SCR_009171 | EM estimation of haplotype frequencies and LD calculation | 2026-02-14 02:07:00 | 4 | |||||||
|
EPDT Resource Report Resource Website 1+ mentions |
EPDT (RRID:SCR_009172) | EPDT | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that for detecting linkage/disequilibrium signals # between genetic markers and disease loci, particularly if only one # or a few large pedigrees are available. The strategy differs from # conventional approaches that require at least a moderate number of # families to attain adequate statistical power. The proposed testing # procedure is advantageous in that it provides high statistical power # coupled with reduced sample collection. Furthermore, the proposed # method avoids problems such as potential population stratification # and genetic heterogeneity, and is robust with respect to misspecification # of phenotype. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154301 | SCR_009172 | Extended Pedigree Disequilibrium Test | 2026-02-14 02:07:14 | 1 | |||||||
|
EH Resource Report Resource Website |
EH (RRID:SCR_009168) | EH | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos, unix | is listed by: Genetic Analysis Software | nlx_154291 | SCR_009168 | FASTEHPLUS, EHP, Estimating Haplotype-frequencies EHPLUS | 2026-02-14 02:07:14 | 0 | ||||||||
|
EAGLET Resource Report Resource Website 1+ mentions |
EAGLET (RRID:SCR_009166) | EAGLET | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location. | gene, genetic, genomic, perl, c, linux, macos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154288 | SCR_009166 | Efficient Analysis of Genetic Linkage: Testing and Estimation | 2026-02-14 02:07:08 | 1 | |||||||
|
EASYLINKAGE/EASYLINKAGE-PLUS Resource Report Resource Website 1+ mentions |
EASYLINKAGE/EASYLINKAGE-PLUS (RRID:SCR_009167) | EASYLINKAGE/EASYLINKAGE-PLUS | software resource, software application | Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies. | gene, genetic, genomic, perl, v5.8 (program can be provided as perl script or as a compiled exe for the use in windows), ms-windows, (2000/xp), linux | is listed by: Genetic Analysis Software | nlx_154289 | https://omictools.com/easylinkage-tool | http://compbio.charite.de/genetik/hoffmann/easyLINKAGE/ | SCR_009167 | 2026-02-14 02:07:00 | 5 | |||||||
|
DPPH Resource Report Resource Website 1000+ mentions |
DPPH (RRID:SCR_009164) | DPPH | software resource, software application | Software application that is similar to the BPPH program (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, linux, macos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154287 | SCR_009164 | Direct method for Perfect Phylogeney Haplotyping | 2026-02-14 02:07:14 | 1148 | |||||||
|
GREGOR Resource Report Resource Website 10+ mentions |
GREGOR (RRID:SCR_009165) | GREGOR | software resource, software application | Software program that allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, ms-dos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154364 | http://gnome.agrenv.mcgill.ca/tinker/gregor.htm | SCR_009165 | 2026-02-14 02:06:46 | 47 | |||||||
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Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | software resource, source code, data processing software, software application | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-02-14 02:00:22 | 6933 | ||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | data processing software, data analysis software, source code, software application, software resource, simulation software | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-02-14 02:00:42 | 126 |
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