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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TDT/S-TDT Resource Report Resource Website 1+ mentions |
TDT/S-TDT (RRID:SCR_005548) | TDT/S-TDT | software application, software resource | Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, (95/nt) | is listed by: Genetic Analysis Software | nlx_154679 | SCR_005548 | Transmission Disequilibrium Test and Sib Transmission Disequilibrium Test | 2026-02-15 09:18:59 | 3 | ||||||||
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PEDSCRIPT Resource Report Resource Website |
PEDSCRIPT (RRID:SCR_004571) | PEDSCRIPT | software application, software resource | Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154528 | SCR_004571 | 2026-02-15 09:18:50 | 0 | |||||||||
|
HAPLOBLOCKFINDER Resource Report Resource Website 1+ mentions |
HAPLOBLOCKFINDER (RRID:SCR_005844) | HAPLOBLOCKFINDER | software application, software resource | Software package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine. (entry from Genetic Analysis Software) | gene, genetic, genomic, c and perl, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154380 | SCR_005844 | 2026-02-15 09:19:05 | 6 | |||||||||
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HAPMIXMAP Resource Report Resource Website |
HAPMIXMAP (RRID:SCR_006066) | HAPMIXMAP | software application, software resource | Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154391 | SCR_006066 | 2026-02-15 09:19:09 | 0 | |||||||||
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LDHAT Resource Report Resource Website 10+ mentions |
LDHAT (RRID:SCR_006298) | LDHAT | software application, software resource | Software package for the analysis of recombination rates from population genetic data (entry from Genetic Analysis Software) | gene, genetic, genomic, c, dos | is listed by: Genetic Analysis Software | nlx_154423 | SCR_006298 | 2026-02-15 09:19:24 | 45 | |||||||||
|
VARSCAN Resource Report Resource Website 1000+ mentions |
VARSCAN (RRID:SCR_006849) | VarScan | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java, illumina, solid, life/pgm, roche/454, next-generation sequencing, variant, mutation caller, exome, whole-genome, snp, copy number alteration, somatic mutation, subclonal mutation, mutation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154687, biotools:varscan, OMICS_00094 | http://varscan.sourceforge.net/ http://dkoboldt.github.io/varscan/ https://bio.tools/varscan https://sources.debian.org/src/varscan/ |
http://genome.wustl.edu/software/varscan | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-02-15 09:19:20 | 1769 | ||||
|
LSP Resource Report The record is no longer available at this source. |
LSP (RRID:SCR_007059) | LSP | software application, software resource | Software application that is part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software) | gene, genetic, genomic, c and pascal, unix, vms, ms-dos, os2 | is listed by: Genetic Analysis Software | SCR_007059 | Linkage Setup Program | 2026-02-15 09:19:21 | 0 | |||||||||
|
RTDT Resource Report Resource Website 10+ mentions |
RTDT (RRID:SCR_007336) | RTDT | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, matlab, c++ | is listed by: Genetic Analysis Software | nlx_154579 | SCR_007336 | Robust Transmission/Disequilibrium Test | 2026-02-15 09:19:24 | 17 | ||||||||
|
TKMAP Resource Report Resource Website |
TKMAP (RRID:SCR_007457) | TKMAP | software application, software resource | Software program for drawing genetic maps (entry from Genetic Analysis Software) | gene, genetic, genomic, based on biotk which is based on tcl/tk | is listed by: Genetic Analysis Software | nlx_154026 | SCR_007457 | 2026-02-15 09:19:36 | 0 | |||||||||
|
BEAM Resource Report Resource Website 500+ mentions |
BEAM (RRID:SCR_007258) | BEAM | software application, software resource | Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, dos | is listed by: Genetic Analysis Software | nlx_154240 | SCR_007258 | Bayesian Epistasis Association Mapping | 2026-02-15 09:19:31 | 651 | ||||||||
|
LDSELECT Resource Report Resource Website 10+ mentions |
LDSELECT (RRID:SCR_007010) | LDSELECT | software application, software resource | Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, 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:ld_select, nlx_154426 | https://bio.tools/ld_select | SCR_007010 | 2026-02-15 09:19:21 | 15 | |||||||
|
INTEGRAYEDMAP Resource Report Resource Website |
INTEGRAYEDMAP (RRID:SCR_007489) | INTEGRAYEDMAP | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data. | gene, genetic, genomic, ms-windows, (nt/2000/xp profession/), require either, oracle rdbms, or, mysql | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154099 | ftp://cggc.agtec.uga.edu/IntegratedMap/ | SCR_007489 | 2026-02-15 09:19:36 | 0 | |||||||
|
LDMAP Resource Report Resource Website 1+ mentions |
LDMAP (RRID:SCR_006308) | LDMAP | software application, software resource | Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, solaris | is listed by: Genetic Analysis Software | nlx_154425 | SCR_006308 | 2026-02-15 09:19:13 | 8 | |||||||||
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JENTI Resource Report Resource Website |
JENTI (RRID:SCR_009053) | JENTI | software application, software resource | An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way. (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154033 | SCR_009053 | 2026-02-15 09:20:01 | 0 | |||||||||
|
COMBIN Resource Report Resource Website |
COMBIN (RRID:SCR_009050) | COMBIN | software application, software resource | Software application designed for the construction of highly saturated linkage maps, based on BC1, DH, Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supported. (entry from Genetic Analysis Software) | gene, genetic, genomic, visual basic 5, ms-windows, (95/98/nt) | is listed by: Genetic Analysis Software | nlx_154025 | http://www.dpw.wau.nl/pv/pub/combin/ | SCR_009050 | 2026-02-15 09:20:02 | 0 | ||||||||
|
ARLEQUIN Resource Report Resource Website 5000+ mentions |
ARLEQUIN (RRID:SCR_009051) | ARLEQUIN | software application, software resource | An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, (95/98/nt/2000/xp) | is listed by: Genetic Analysis Software | nlx_154029 | SCR_009051 | this software is about the study of genetic polymorphism.), a character of the Italian Commedia dell''Arte. He has many aspects, but can switch among them very easily according to needs and necessities. Similarly, (French translation of Arlecchino | 2026-02-15 09:19:56 | 5536 | ||||||||
|
GRONLOD Resource Report Resource Website |
GRONLOD (RRID:SCR_009049) | GRONLOD | software application, software resource | Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood. (entry from Genetic Analysis Software) | gene, genetic, genomic, prolog, ms-windows, (3.1/95/nt) | is listed by: Genetic Analysis Software | nlx_154024 | SCR_009049 | GRONingen university LOR score calculation | 2026-02-15 09:20:01 | 0 | ||||||||
|
SNP ASSISTANT Resource Report Resource Website |
SNP ASSISTANT (RRID:SCR_009048) | SNP ASSISTANT | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects. | gene, genetic, genomic, c++, ms-windows, (95 and newer) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154023 | SCR_009048 | 2026-02-15 09:19:37 | 0 | ||||||||
|
PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software application, software resource | Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (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_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-02-15 09:20:02 | 1 | ||||||||
|
PATH Resource Report Resource Website 100+ mentions |
PATH (RRID:SCR_009042) | PATH | software application, software resource | Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, ms-windows, linux, FASEB list | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154015 | SCR_009042 | 2026-02-15 09:19:56 | 253 |
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