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http://csbio.unc.edu/CCstatus/index.py

Core focused on systems genetics approach to understanding diseases, development, aging, and fertility in mouse. Projects range from development of new community resources, such as Collaborative Cross, to development of tools and assays for measuring genetic diversity and discerning genomic structure. Collaborative Cross is reference population for mapping multigenic traits that would be free of population structure and it is new panel of recombinant inbred lines generated by randomizing genetic diversity of existing inbred mouse resources.

Proper citation: University of North Carolina Systems Genetics Core Facility (RRID:SCR_016401) Copy   

•   Source: SciCrunch Registry

http://bpc.facilities.northwestern.edu

Facility dedicated to help to determine behavioral effects of genetic manipulations, potential pharmaceuticals, aging, and other manipulations upon normal behavior, and learning and memory capacities of rodents used as model systems. Provides mouse and rat stereotaxic surgery, helps design behavioral studies.

Proper citation: Northwestern University Behavioral Phenotyping Core Facility (RRID:SCR_017765) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/ccle/

A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

Proper citation: Cancer Cell Line Encyclopedia (RRID:SCR_013836) Copy   

•   Source: SciCrunch Registry

https://www.ars-grin.gov/npgs/

Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.

Proper citation: National Plant Germplasm System (NPGS) (RRID:SCR_016785) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy   

•   Source: SciCrunch Registry

http://mmrrc.ucdavis.edu/

Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.

Proper citation: University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) Copy   

•   Source: SciCrunch Registry

http://www.mmrrc.missouri.edu/

Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains.

Proper citation: Mutant Mouse Resource and Research Center - University of Missouri (RRID:SCR_016447) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)

Proper citation: COMPOSITELD (RRID:SCR_013132) Copy   

•   Source: SciCrunch Registry

http://www.vet.upenn.edu/research/core-resources-facilities/referral-center-for-animal-models

Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients.

Proper citation: Referral Center for Animal Models of Human Genetic Diseases (RRID:SCR_016453) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

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)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

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)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://eyegene.ophthy.med.umich.edu/madeline/

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.

Proper citation: MADELINE (RRID:SCR_001979) Copy   

•   Source: SciCrunch Registry

http://www.depressiontools.org/

Online instrument that estimates whether a biomarker predicting outcome of depression treatment is likely to be clinically significant.

Proper citation: DepressionTools.org Clinical Significance Calculator (RRID:SCR_003873) Copy   

•   Source: SciCrunch Registry

http://analysis2.bio-x.cn/myAnalysis.php

A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

Proper citation: SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) Copy   

•   Source: SciCrunch Registry

http://cbl-gorilla.cs.technion.ac.il/

A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.

Proper citation: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

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https://cran.r-project.org/web/packages/adegenet/index.html

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)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/node/252

THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu.

Proper citation: FaceBase Biorepository (RRID:SCR_006001) Copy   

•   Source: SciCrunch Registry