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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
OLORIN Resource Report Resource Website |
OLORIN (RRID:SCR_002015) | OLORIN | software resource, software application | 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 | 2026-02-13 10:54:58 | 0 | ||||||
|
SIMIBD Resource Report Resource Website |
SIMIBD (RRID:SCR_002094) | SIMIBD | software resource, software application | 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 | 2026-02-13 10:54:58 | 0 | ||||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software resource, software application | 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 | 2026-02-13 10:54:55 | 370 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software resource, software application | 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 | 2026-02-13 10:54:54 | 45 | |||||
|
PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software resource, software application | 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 | 2026-02-13 10:54:58 | 2 | ||||||
|
LAMP Resource Report Resource Website 1000+ mentions |
LAMP (RRID:SCR_001740) | LAMP | software resource, software application | 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 | 2026-02-13 10:54:54 | 1157 | ||||||
|
SYZYGY Resource Report Resource Website 1+ mentions |
SYZYGY (RRID:SCR_002157) | Syzygy | software resource, software application | 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 | 2026-02-13 10:54:59 | 5 | ||||||
|
HWESTRATA Resource Report Resource Website |
HWESTRATA (RRID:SCR_001097) | HWESTRATA | software resource, software application | 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 | 2026-02-13 10:54:49 | 0 | ||||||||
|
HAPSCOPE Resource Report Resource Website |
HAPSCOPE (RRID:SCR_000838) | HAPSCOPE | software resource, software application | 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 | 2026-02-13 10:54:45 | 0 | ||||||||
|
COMDS Resource Report Resource Website |
COMDS (RRID:SCR_000832) | COMDS | software resource, software application | 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 | 2026-02-13 10:54:45 | 0 | ||||||||
|
GAS2 Resource Report Resource Website |
GAS2 (RRID:SCR_001126) | GAS2 | software resource, software application | 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 | 2026-02-13 10:54:48 | 0 | |||||||
|
CHAPLIN Resource Report Resource Website 1+ mentions |
CHAPLIN (RRID:SCR_000833) | CHAPLIN | software resource, software application | 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 | 2026-02-13 10:54:44 | 2 | |||||||
|
CRIMAP Resource Report Resource Website 1+ mentions |
CRIMAP (RRID:SCR_000834) | CRIMAP | software resource, software application | 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 | 2026-02-13 10:54:45 | 5 | ||||||
|
EQTL EXPLORER Resource Report Resource Website 1+ mentions |
EQTL EXPLORER (RRID:SCR_001123) | EQTL EXPLORER | software resource, software application | 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 | 2026-02-13 10:54:49 | 2 | |||||||
|
TDT-PC Resource Report Resource Website |
TDT-PC (RRID:SCR_001116) | TDT-PC | software resource, software application | 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 | 2026-02-13 10:54:49 | 0 | ||||||
|
BEAGLE Resource Report Resource Website 1000+ mentions |
BEAGLE (RRID:SCR_001789) | BEAGLE | software resource, software application | Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac). | gene, genetic, genomic, java, ms-windows, linux, unix, solaris, macos, identity by descent, genotype, haplotype |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17924348 PMID:17326099 PMID:21310274 DOI:10.1086/521987 |
Free, Available for download, Freely available | nlx_154238, OMICS_00052, OMICS_00201 | https://sources.debian.org/src/beagle/ | https://www.stat.auckland.ac.nz/%7Ebrowning/beagle/beagle.html | SCR_001789 | BEAGLE Genetic Analysis Software Package | 2026-02-13 10:54:55 | 2197 | ||||
|
CYRILLIC Resource Report Resource Website 50+ mentions |
CYRILLIC (RRID:SCR_001823) | Cyrillic | software resource, software application, commercial organization | Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages. | gene, genetic, genomic, visual c++, ms-windows, pedigree, linkage analysis, risk analysis, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
PMID:1973333 | Free, Available for download, Freely available | nlx_154279, OMICS_00208 | http://www.cyrillicsoftware.com | SCR_001823 | CyrillicSoftware | 2026-02-13 10:54:55 | 52 | |||||
|
CLUSTAG Resource Report Resource Website 1+ mentions |
CLUSTAG (RRID:SCR_001816) | CLUSTAG | software resource, software application | Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment. | gene, genetic, genomic, java, hierarchical clustering, single nucleotide polymorphism, windows, unix |
is listed by: Genetic Analysis Software has parent organization: Hong Kong Baptist University; Hong Kong; China |
PMID:15585525 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154273 | http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html | SCR_001816 | CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs | 2026-02-13 10:54:55 | 1 | |||||
|
PEDIGREE-VISUALIZER Resource Report Resource Website |
PEDIGREE-VISUALIZER (RRID:SCR_000842) | PEDIGREE-VISUALIZER | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154521 | SCR_000842 | 2026-02-13 10:54:45 | 0 | |||||||||
|
PEDPHASE Resource Report Resource Website |
PEDPHASE (RRID:SCR_000843) | PEDPHASE | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154525 | SCR_000843 | 2026-02-13 10:54:44 | 0 |
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