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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Simons Simplex Collection Resource Report Resource Website 1+ mentions |
Simons Simplex Collection (RRID:SCR_004644) | SSC | material resource, cell repository, biomaterial supply resource | Repository of genetic samples from approximately 3,000 families, each of which has one child affected with an Autism Spectrum Disorder (ASD) and parents unaffected with ASD. A central database characterizing all of the study subjects is available to any qualified researcher and biospecimens are freely available to SFARI grant holders, and to other researchers on a modest fee-for-use basis. Each genetic sample will have an associated collection of data that provides a precise characterization of the individual (phenotype). Rigorous phenotyping will maximize the value of the resource for a wide variety of future research projects into the causes and mechanisms of autism. The Simons Simplex Collection is operated by SFARI in collaboration with twelve university-affiliated research clinics. | phenotype, genetic, cell line, fibroblast, dna, plasma |
is listed by: One Mind Biospecimen Bank Listing has parent organization: SFARI - Simons Foundation Autism Research Initiative |
Autism, Autism Spectrum Disorder, Unaffected parent | Public: Central database is available to any qualified researcher and biospecimens are freely available to SFARI grant holders, And to other researchers on a modest fee-for-use basis. | nlx_64171 | https://sfari.org/simons-simplex-collection | SCR_004644 | 2026-02-15 09:18:47 | 2 | ||||||
|
EM-DECODER Resource Report Resource Website 1+ mentions |
EM-DECODER (RRID:SCR_000023) | EM-DECODER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154297 | SCR_000023 | 2026-02-15 09:17:51 | 1 | ||||||||
|
ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/ https://sources.debian.org/src/r-cran-adegenet/ |
SCR_000825 | R/ADEGENET | 2026-02-15 09:17:59 | 20 | |||||
|
GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-02-15 09:18:09 | 451 | |||||
|
OLORIN Resource Report Resource Website |
OLORIN (RRID:SCR_002015) | OLORIN | software application, software resource | An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any platform with java 1.6 or later, next generation sequencing, variant, haplotype, allele frequency, java swing |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: SourceForge |
PMID:23052039 | Free, Available for download, Freely available | nlx_154503, OMICS_01556 | http://sourceforge.net/p/olorin/ | SCR_002015 | 2026-02-15 09:18:13 | 0 | ||||||
|
SIMIBD Resource Report Resource Website |
SIMIBD (RRID:SCR_002094) | SIMIBD | 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, c, unix, (sunos/solaris/hp/dec-unix) | is listed by: Genetic Analysis Software | PMID:9002040 | Free, Available for download, Freely available | nlx_154622 | http://watson.hgen.pitt.edu/register/soft_doc.html, http://watson.hgen.pitt.edu/~davis/ | SCR_002094 | 2026-02-15 09:18:14 | 0 | ||||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-02-15 09:18:10 | 370 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-02-15 09:18:09 | 45 | |||||
|
PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software application, software resource | Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. | gene, genetic, genomic, genealogy, pedigree, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
PMID:20433770 PMID:9521925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pedhunter, OMICS_00211, nlx_154518 | https://bio.tools/pedhunter | SCR_002031 | 2026-02-15 09:18:13 | 2 | ||||||
|
LAMP Resource Report Resource Website 1000+ mentions |
LAMP (RRID:SCR_001740) | LAMP | software application, software resource | Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern. | gene, genetic, genomic, c++, unix, linux, windows, macos, linkage, association, modeling, pedigree |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:16642434 | Free, Available for download, Freely available | nlx_154103 | SCR_001740 | Linkage and Association Modeling in Pedigrees | 2026-02-15 09:18:10 | 1157 | ||||||
|
SYZYGY Resource Report Resource Website 1+ mentions |
SYZYGY (RRID:SCR_002157) | Syzygy | software application, software resource | A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software) | gene, genetic, genomic, variant calling, snp, indel, allele frequency, single-marker association, group-wise marker, quality control, variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:21983784 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154668, OMICS_02166 | SCR_002157 | Syzygy - SNP and indel calling for pooled and individual targeted resequencing studies | 2026-02-15 09:18:15 | 5 | ||||||
|
HWESTRATA Resource Report Resource Website |
HWESTRATA (RRID:SCR_001097) | HWESTRATA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, solaris, ms-windows, (xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154405 | SCR_001097 | 2026-02-15 09:18:02 | 0 | ||||||||
|
HAPSCOPE Resource Report Resource Website |
HAPSCOPE (RRID:SCR_000838) | HAPSCOPE | software application, software resource | Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:12466546 | nlx_154393 | SCR_000838 | 2026-02-15 09:18:00 | 0 | ||||||||
|
GENEHUNTER SAD Resource Report Resource Website |
GENEHUNTER SAD (RRID:SCR_000831) | GENEHUNTER SAD | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154198 | SCR_000831 | 2026-02-15 09:18:00 | 0 | ||||||||
|
COMDS Resource Report Resource Website |
COMDS (RRID:SCR_000832) | COMDS | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software) | gene, genetic, genomic, sun fortran, (the command fsplit is needed), unix, sunos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154255 | SCR_000832 | 2026-02-15 09:17:59 | 0 | ||||||||
|
GAS2 Resource Report Resource Website |
GAS2 (RRID:SCR_001126) | GAS2 | software application, software resource | Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77 | is listed by: Genetic Analysis Software | PMID:16408254 | nlx_154323 | SCR_001126 | statistical significance in Genomewide Association Studies in 2-stage | 2026-02-15 09:18:03 | 0 | |||||||
|
CHAPLIN Resource Report Resource Website 1+ mentions |
CHAPLIN (RRID:SCR_000833) | CHAPLIN | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran90, (cvf 6.6) with imsl routines, ms-windows, (2000/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154266 | SCR_000833 | Case-control HAPLotype INference package | 2026-02-15 09:18:00 | 2 | |||||||
|
CRIMAP Resource Report Resource Website 1+ mentions |
CRIMAP (RRID:SCR_000834) | CRIMAP | software application, software resource | Software application for constructing multilocus linkage map (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-windows, xp | is listed by: Genetic Analysis Software | PMID:7750973 | Source code available | nlx_154276 | http://compgen.rutgers.edu/Crimap/ | SCR_000834 | 2026-02-15 09:18:00 | 5 | ||||||
|
EQTL EXPLORER Resource Report Resource Website 1+ mentions |
EQTL EXPLORER (RRID:SCR_001123) | EQTL EXPLORER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | PMID:16357031 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154018 | SCR_001123 | 2026-02-15 09:18:03 | 2 | |||||||
|
TDT-PC Resource Report Resource Website |
TDT-PC (RRID:SCR_001116) | TDT-PC | software application, software resource | Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, ms-dos, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
PMID:11443734 | nlx_154677, biotools:tdt_power_calculator | https://bio.tools/tdt_power_calculator | SCR_001116 | Transmission Disequilibrium Test Power Calculator, TDT Power Calculator | 2026-02-15 09:18:03 | 0 |
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