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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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COPE Resource Report Resource Website 500+ mentions |
COPE (RRID:SCR_009153) | COPE | software application, software resource | Software application that includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. (entry from Genetic Analysis Software) | gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is parent organization of: COPE: Cytokines and Cells Online Pathfinder Encyclopaedia |
nlx_154274 | SCR_009153 | SciCrunch Registry | COllaborative Pedigree drawing Environment | 2026-11-07 12:03:24 | 852 | ||||||||
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CHROMOSCAN Resource Report Resource Website 1+ mentions |
CHROMOSCAN (RRID:SCR_009151) | CHROMOSCAN | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that is an implementation of a genome-based scan statistic that detects genomic regions. | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154270 | http://www.epidkardia.sph.umich.edu/software/chromoscan/ | SCR_009151 | SciCrunch Registry | 2026-11-07 12:03:42 | 2 | |||||||
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CHIAMO Resource Report Resource Website 1+ mentions |
CHIAMO (RRID:SCR_009150) | CHIAMO | software application, software resource | Software application for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154269 | http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html | SCR_009150 | SciCrunch Registry | 2026-11-07 12:03:44 | 2 | ||||||||
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CHECKMATRIX Resource Report Resource Website 1+ mentions |
CHECKMATRIX (RRID:SCR_009149) | CHECKMATRIX | software application, software resource | Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software) | gene, genetic, genomic, python | is listed by: Genetic Analysis Software | nlx_154268 | SCR_009149 | SciCrunch Registry | PY_MATRIX_D | 2026-11-07 12:03:24 | 9 | ||||||||
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CFC Resource Report Resource Website |
CFC (RRID:SCR_009146) | CFC | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. General-purpose program for monitoring genetic diversity. CFC allows for several pedigree analyses such as: (1) computing inbreeding coefficients and relationships; (2) computing average relationships very quickly within and between specified groups of individuals; (3) computing average relatedness; (4) ancestral decomposition of the average or the individual inbreeding coefficient; (5) ancestral decomposition of the average coancestry; (6) optimizing matings to minimize the average inbreeding coefficients in the next generation; (7) computing founder equivalent, founder genome equivalent and effective number of non-founders; (8) computing numerator relationship matrix, its Cholesky decomposition and its inverse; (9) providing useful information on the structure of pedigrees. | gene, genetic, genomic, visual c++, ms-windows, (98/nt/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154264 | SCR_009146 | SciCrunch Registry | Inbreeding (F) and Coancestry, Contribution | 2026-11-07 12:03:44 | 0 | |||||||
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CEPH2MAP Resource Report Resource Website |
CEPH2MAP (RRID:SCR_009144) | CEPH2MAP | software application, software resource | Software application developed from crimap v2.4 for use with the map suite of programs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154263 | SCR_009144 | SciCrunch Registry | 2026-11-07 12:03:42 | 0 | |||||||||
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EVOKER Resource Report Resource Website 1+ mentions |
EVOKER (RRID:SCR_009145) | EVOKER | software application, software resource | A graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies. It provides a solution to the computational and storage problems related to being able to work with the huge volumes of data generated by such projects by implementing a compact, binary format that allows rapid access to data, even with hundreds of thousands of observations. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, perl | is listed by: Genetic Analysis Software | nlx_154305 | SCR_009145 | SciCrunch Registry | 2026-11-07 12:03:24 | 8 | |||||||||
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CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software application, software resource | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | SciCrunch Registry | Case-Control association analysis with RELlated individuals | 2026-11-07 12:03:44 | 0 | |||||||
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Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, software resource, source code | 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 | SciCrunch Registry | 2026-11-07 12:02:23 | 12 | ||||
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Genotype-IBD Sharing Test Resource Report Resource Website 100+ mentions |
Genotype-IBD Sharing Test (RRID:SCR_006257) | GIST | resource, software application, software resource | Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix. | identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, association |
is listed by: Genetic Analysis Software has parent organization: Vanderbilt University; Tennessee; USA |
Vanderbilt Diabetes Center ; NHGRI HG00376; NIDDK DK62370; NHGRI N01-HG-15465 |
PMID:14872409 | nlx_154133 | http://phg.mc.vanderbilt.edu/content/gist | SCR_006257 | SciCrunch Registry | 2026-11-07 12:02:49 | 120 | ||||||
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LDGROUP Resource Report Resource Website |
LDGROUP (RRID:SCR_006282) | software application, software resource | Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154422, SCR_009368, nlx_154590 | http://www.fumihiko.takeuchi.name/publications.html | SCR_006282 | SciCrunch Registry | R/LDGROUP | 2026-11-07 12:02:13 | 0 | ||||||||
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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 | SciCrunch Registry | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-11-07 12:01:53 | 0 | |||||||
|
Body Mass Index Calculator Resource Report Resource Website |
Body Mass Index Calculator (RRID:SCR_000122) | BMI Calculator | analysis service resource, data analysis service, production service resource, service resource | Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women. | adult human, body mass, male, female |
is listed by: NIDDK Information Network (dkNET) is listed by: Genetic Analysis Software has parent organization: National Heart Lung and Blood Institute |
NHLBI | Free, Public | nlx_152731 | SCR_000122 | SciCrunch Registry | Calculate Your Body Mass Index | 2026-11-07 12:02:01 | 0 | ||||||
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HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | analysis service resource, data analysis service, production service resource, service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | SciCrunch Registry | 2026-11-07 12:01:58 | 125 | ||||||
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MADELINE Resource Report Resource Website 1+ mentions |
MADELINE (RRID:SCR_001979) | MADELINE | service resource, software application, software resource | Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. | gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:17488757 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154446, OMICS_00210 | http://eyegene.ophthy.med.umich.edu/#madeline | SCR_001979 | SciCrunch Registry | Madeline | 2026-11-07 12:02:22 | 5 | |||||
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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 | SciCrunch Registry | 2026-11-07 12:03:24 | 1 | ||||||||
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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 | SciCrunch Registry | 2026-11-07 12:03:00 | 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 | SciCrunch Registry | 2026-11-07 12:03:23 | 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 | SciCrunch Registry | 2026-11-07 12:03:26 | 0 | ||||||||
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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 | SciCrunch Registry | Case-control HAPLotype INference package | 2026-11-07 12:03:27 | 2 |
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