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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-04 09:40:15 | 0 | ||||||||
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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 | 2026-08-04 09:40:14 | 0 | ||||||||
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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 | 2026-08-04 09:40:14 | 0 | ||||||||
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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 | 2026-08-04 09:40:19 | 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 | 2026-08-04 09:40:14 | 2 | |||||||
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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 | 2026-08-04 09:40:14 | 5 | ||||||
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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 | 2026-08-04 09:40:19 | 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 | 2026-08-04 09:40:18 | 0 | ||||||
|
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 | 2026-08-04 09:40:14 | 20 | |||||
|
TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software application, software resource | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-08-04 09:40:22 | 7 | ||||
|
BEAGLE Resource Report Resource Website 1000+ mentions |
BEAGLE (RRID:SCR_001789) | BEAGLE | software application, software resource | 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 | 2026-08-04 09:40:28 | 2197 | ||||
|
CYRILLIC Resource Report Resource Website 50+ mentions |
CYRILLIC (RRID:SCR_001823) | Cyrillic | software application, commercial organization, software resource | 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 | 2026-08-04 09:40:28 | 52 | |||||
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CLUSTAG Resource Report Resource Website 1+ mentions |
CLUSTAG (RRID:SCR_001816) | CLUSTAG | software application, software resource | 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 | 2026-08-04 09:40:29 | 1 | |||||
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PEDIGREE-VISUALIZER Resource Report Resource Website |
PEDIGREE-VISUALIZER (RRID:SCR_000842) | PEDIGREE-VISUALIZER | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154521 | SCR_000842 | 2026-08-04 09:40:15 | 0 | |||||||||
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PEDPHASE Resource Report Resource Website |
PEDPHASE (RRID:SCR_000843) | PEDPHASE | software application, software resource | 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 | 2026-08-04 09:40:15 | 0 | ||||||||
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LOCUSMAP Resource Report Resource Website |
LOCUSMAP (RRID:SCR_000840) | LOCUSMAP | software application, software resource | Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 90/95, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154434, biotools:locusmap | https://bio.tools/locusmap | SCR_000840 | 2026-08-04 09:40:15 | 0 | ||||||||
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RHMAPPER Resource Report Resource Website |
RHMAPPER (RRID:SCR_000845) | RHMAPPER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154576 | SCR_000845 | 2026-08-04 09:40:15 | 0 | ||||||||
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GS-EM Resource Report Resource Website |
GS-EM (RRID:SCR_003992) | GS-EM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154366 | SCR_003992 | GenoSpectrum Expectation-Maximuzation | 2026-08-04 09:41:02 | 0 | ||||||||
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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 | 2026-08-04 09:40:33 | 0 | ||||||
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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 | 2026-08-04 09:40:32 | 2 |
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