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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GGSD Resource Report Resource Website |
GGSD (RRID:SCR_013129) | software application, software resource | Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, php, perl, web-based | is listed by: Genetic Analysis Software | nlx_154355 | SCR_013129 | Generic Genetic Studies Database | 2026-02-15 09:20:24 | 0 | |||||||||
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CHROMSCAN Resource Report Resource Website 1+ mentions |
CHROMSCAN (RRID:SCR_013131) | CHROMSCAN | software application, software resource | A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154272 | SCR_013131 | 2026-02-15 09:20:38 | 2 | |||||||||
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BOREL Resource Report Resource Website 1+ mentions |
BOREL (RRID:SCR_013135) | software application, software resource | Software application for inference of genealogical relationships from genetic data, including sibship inference. | gene, genetic, genomic, c, unix, (dec-unix/..) |
is listed by: Genetic Analysis Software is related to: PANGAEA |
nlx_154197 | http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml | ftp://ftp.u.washington.edu/pub/user-supported/pangaea/PANGAEA/BOREL | SCR_013135 | 2026-02-15 09:20:38 | 8 | ||||||||
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GASSOC Resource Report Resource Website 10+ mentions |
GASSOC (RRID:SCR_013136) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sunos, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154077 | SCR_013136 | Genetic ASSOCiation analysis software for cases and parent | 2026-02-15 09:20:43 | 13 | ||||||||
|
SNPMSTAT Resource Report Resource Website |
SNPMSTAT (RRID:SCR_013339) | SNPMSTAT | software application, software resource | A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154647 | SCR_013339 | SNP Missing data STATistics | 2026-02-15 09:20:26 | 0 | ||||||||
|
MECPM Resource Report Resource Website |
MECPM (RRID:SCR_013341) | MECPM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154070 | SCR_013341 | Maximum Entropy Conditional Probability Moldeling | 2026-02-15 09:20:40 | 0 | ||||||||
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MAOS Resource Report Resource Website 10+ mentions |
MAOS (RRID:SCR_013351) | software application, software resource | Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++ | is listed by: Genetic Analysis Software | nlx_154452 | SCR_013351 | Meta-Analysis with Overlapping Subjects | 2026-02-15 09:20:27 | 25 | |||||||||
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ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-02-15 09:17:52 | 0 | |||||||
|
Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 | ||||
|
SNPSTATS Resource Report Resource Website 500+ mentions |
SNPSTATS (RRID:SCR_002142) | SNPStats | data analysis service, analysis service resource, software resource, source code, production service resource, service resource | A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate) | gene, genetic, genomic, single nucleotide polymorphism, association study, genetic, epidemiology, allele, frequency, genotype, allele frequency, genotype frequency, hardy-weinberg equilibrium, linkage disequilibrium, haplotype frequency, haplotype, interaction, haplotypes-covariate, association, linear regression, logistic regression, inheritance model, co-dominant, dominant, recessive, over-dominant, additive, gene-gene, gene-environment |
is listed by: Genetic Analysis Software has parent organization: Autonomous University of Barcelona; Barcelona; Spain |
PMID:16720584 | Free, Available for download, Freely available | nlx_154650 | http://bioinfo.iconcologia.net/snpstats/ | SCR_002142 | SNP STATisticS | 2026-02-16 09:45:40 | 619 | |||||
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools https://github.com/samtools/htslib https://bio.tools/samtools https://sources.debian.org/src/samtools/ |
http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-02-16 09:45:44 | 30156 | |||
|
Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | software application, data processing software, data analysis software, source code, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). | qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping |
is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics |
Wellcome Trust | PMID:11050180 DOI:10.1073/pnas.230304397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152594 | http://www.well.ox.ac.uk/~rmott/happy.html | https://sources.debian.org/src/r-other-mott-happy.hbrem/ | SCR_001395 | reconstructing HAPlotYpes | 2026-02-16 09:45:28 | 46 | |||
|
GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software resource, software toolkit, software library | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/ https://cran.r-project.org/web/packages/GenABEL/index.html https://sources.debian.org/src/probabel/ |
SCR_001842 | GenABEL package, R/GENABEL | 2026-02-16 09:45:36 | 506 | |||||
|
PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | software application, data processing software, software toolkit, data analysis software, software resource | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/ https://www.cog-genomics.org/plink/1.9/general_usage#cite https://sources.debian.org/src/plink/ |
http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-02-16 09:45:35 | 15344 | |||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | software application, data processing software, data analysis software, software resource, time-series analysis software | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA https://bio.tools/GMA |
http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | Granger Mediation Analysis | 2026-02-16 09:47:21 | 0 | |||
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HAP-SAMPLE Resource Report Resource Website 1+ mentions |
HAP-SAMPLE (RRID:SCR_009234) | HAP-SAMPLE | software application, data analysis service, analysis service resource, software resource, production service resource, service resource | Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154392 | SCR_009234 | 2026-02-16 09:47:22 | 4 | |||||||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software resource, software application, software toolkit, software library | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp https://cran.r-project.org/src/contrib/Archive/qtlbim/ https://bio.tools/qtlbim |
http://www.qtlbim.org/ | SCR_009375 | 2026-02-16 09:47:23 | 2 | ||||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | software application, software resource, commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-02-16 09:47:09 | 1 | ||||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-02-16 09:48:33 | 0 | ||||||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-02-16 09:47:00 | 3 |
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