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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-02-15 09:18:10 | 1899 | ||||||
|
POLYMUTT Resource Report Resource Website 1+ mentions |
POLYMUTT (RRID:SCR_002051) | Polymutt | software application, software resource | Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation sequencing, mutation, de novo point mutation, single nucleotide variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:23055937 | Free, Available for download, Freely available | OMICS_00088, nlx_154539 | SCR_002051 | POLYmorphism and de novo MUTaTion call in families with sequencing data | 2026-02-15 09:18:14 | 3 | ||||||
|
POLYMORPHISM Resource Report Resource Website |
POLYMORPHISM (RRID:SCR_000828) | software application, software resource | Software application for calculating the heterozygosity, PIC, and LIC values for polymorphic markers (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154052 | SCR_000828 | 2026-02-15 09:17:59 | 0 | |||||||||
|
EDAC Resource Report Resource Website 1+ mentions |
EDAC (RRID:SCR_000829) | EDAC | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154078 | http://www.biostat.wustl.edu/~gc/cgi-bin/calcpwr.cgi | SCR_000829 | power calculator for Extremely Discordant And Concordant sibpairs | 2026-02-15 09:17:59 | 2 | ||||||
|
2LD Resource Report Resource Website |
2LD (RRID:SCR_000826) | 2LD | software application, software resource | Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers. | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | PMID:14871868 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154006 | http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm | SCR_000826 | 2026-02-15 09:17:59 | 0 | ||||||
|
SQTL Resource Report Resource Website |
SQTL (RRID:SCR_000827) | SQTL | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | Free, Available for download, Freely available | nlx_154032 | SCR_000827 | Semiparametric QTL mapping in general pedigrees | 2026-02-15 09:17:59 | 0 | |||||||
|
EIGENSOFT/EIGENSTRAT Resource Report Resource Website 1+ mentions |
EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) | EIGENSOFT/EIGENSTRAT | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | Free, Available for download, Freely available | nlx_154296 | http://www.hsph.harvard.edu/faculty/alkes-price/software/ | SCR_001357 | 2026-02-15 09:18:05 | 1 | |||||||
|
BIRDSUITE Resource Report Resource Website 10+ mentions |
BIRDSUITE (RRID:SCR_001794) | Birdsuite | software application, software resource | Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs. | gene, genetic, genomic, snp, genotype, copy number polymorphism, copy number variant, affymetrix |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:18776909 | Free, Available for download, Freely available | OMICS_00705, nlx_154245 | SCR_001794 | 2026-02-15 09:18:10 | 43 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel https://sources.debian.org/src/dindel/ |
http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-02-15 09:18:11 | 44 | ||||
|
SOLAR Resource Report Resource Website 10+ mentions |
SOLAR (RRID:SCR_000850) | SOLAR | software application, software resource | A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, c, c++, tcl, unix, (solaris 7-10/solaris x86 8-9/digital unix 4.0e/sg irix), linux, macos, ms-windows | is listed by: Genetic Analysis Software | nlx_154653 | http://www.sfbr.org/Departments/genetics_detail.aspx?p=37 | SCR_000850 | Sequential Oligogenic Linkage Analysis Routines | 2026-02-15 09:18:00 | 22 | |||||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-02-15 09:18:12 | 17 | ||||||
|
MRH Resource Report Resource Website |
MRH (RRID:SCR_000841) | MRH | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154493 | SCR_000841 | Minimum Recombinant Haplotype | 2026-02-15 09:18:00 | 0 | |||||||
|
QTL CAFE Resource Report Resource Website |
QTL CAFE (RRID:SCR_000844) | QTL CAFE | software application, software resource | Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154563 | SCR_000844 | 2026-02-15 09:18:00 | 0 | |||||||||
|
Starbase V2.0 Resource Report Resource Website 500+ mentions |
Starbase V2.0 (RRID:SCR_016303) | web application, software resource | Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes. | visualize, analyze, discover, download, large, genomic, data, set, miRNA, RNA-RNA, protein-RNA, interaction, network, decoding, CLIP-Seq, Degradome-Seq | Ministry of Science and Technology of China ; National Basic Research Program No. 2011CB811300 |
PMID:24297251 | Free, Freely available, Available for download | SCR_016303 | 2026-02-15 09:21:04 | 819 | |||||||||
|
Italian Institute for Genomic Medicine; Turin; Italy Resource Report Resource Website |
Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) | IIGM, HuGeF | data or information resource, topical portal, portal | Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience. | institute, private, research, human, genetic, genomic, epigenomic, immunogenetic, quantitative, biology, computational, neuroscience | is parent organization of: HaTSPiL | SCR_017062 | 2026-02-15 09:21:57 | 0 | ||||||||||
|
PEDPLOT Resource Report Resource Website |
PEDPLOT (RRID:SCR_003843) | PEDPLOT | software application, software resource | Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, postscript, unix, (sparc-solaris 2.5/dec unix 4.0/x86-solaris 2.6) | is listed by: Genetic Analysis Software | nlx_154526 | SCR_003843 | 2026-02-15 09:18:35 | 0 | |||||||||
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PARENTE Resource Report Resource Website 1+ mentions |
PARENTE (RRID:SCR_004717) | PARENTE | software application, software resource | Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154508 | SCR_004717 | 2026-02-15 09:18:48 | 2 | |||||||||
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Multipoint Identical-by-descent Method Resource Report Resource Website |
Multipoint Identical-by-descent Method (RRID:SCR_004676) | MIM | software application, software resource | Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | PMID:9433587 | nlx_154482 | SCR_004676 | 2026-02-15 09:18:47 | 0 | ||||||||
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PEDRAW/WPEDRAW Resource Report Resource Website |
PEDRAW/WPEDRAW (RRID:SCR_004797) | PEDRAW/WPEDRAW | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-dos, ms-windows, x-window | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154527 | SCR_004797 | Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW) | 2026-02-15 09:18:54 | 0 | |||||||
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TDTASP Resource Report Resource Website 1+ mentions |
TDTASP (RRID:SCR_004943) | TDTASP | software application, software resource | Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran95, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154675 | SCR_004943 | Power and Sample-Size Calculations for the TDT and ASP Tests | 2026-02-15 09:18:58 | 3 |
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