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http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/

Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPSCOPE (RRID:SCR_000838) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

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)

Proper citation: GENEHUNTER SAD (RRID:SCR_000831) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/comds

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)

Proper citation: COMDS (RRID:SCR_000832) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

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)

Proper citation: CHAPLIN (RRID:SCR_000833) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimap.shtml

Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

Proper citation: CRIMAP (RRID:SCR_000834) Copy   

•   Source: SciCrunch Registry

Issue

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

http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDIGREE-VISUALIZER (RRID:SCR_000842) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/haplotyping.html

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)

Proper citation: PEDPHASE (RRID:SCR_000843) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/ftp/pub/software/rhmapper/

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)

Proper citation: RHMAPPER (RRID:SCR_000845) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy   

•   Source: SciCrunch Registry

http://www.cpgr.org.za

Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry.

Proper citation: University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility (RRID:SCR_017158) Copy   

•   Source: SciCrunch Registry

https://mugenomicscore.missouri.edu/

Core research facility providing services in high-throughput DNA sequencing that includes staff experience in the construction of libraries for targeted amplicons, miRNA analysis, transcriptome profiling (RNA-Seq), whole exome sequencing (WES), epigenomic and genomic DNA analysis. Services in single cell library preparation are available using the 10x Genomics Chromium X system. In addition, spatial transcriptomics services using Visium HD arrays are provided. The GTC maintain and operate Illumina sequencing platforms; NovaSeq X Plus and MiSeq i100 instruments.

Proper citation: University of Missouri Genomics Technology Core Facility (RRID:SCR_017778) Copy   

•   Source: SciCrunch Registry

https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies

Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma.

Proper citation: Duke University Sequencing and Genomic Technologies Core Facility (RRID:SCR_017748) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/molecular-genomics-shared-resource

Core offers variety of experimental platforms to facilitate genomics research. Accredited as Duke Shared Resource facility offers experience with genetic, genomic and epigenomic study design and technology, working closely with researchers to customize experiments to meet their needs. Applications include 10x Genomics NGS library generation for both single cell and gDNA experiments, DNA methylation microarrays, SNP genotyping and copy number microarrays, and Taqman targeted SNP genotyping.

Proper citation: Duke University Molecular Genomics Core Facility (RRID:SCR_017860) Copy   

•   Source: SciCrunch Registry

https://escore.ucsf.edu/

Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services.

Proper citation: University of California at San Francisco Embryonic Stem Cell Targeting Core Facility (RRID:SCR_017902) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/presto/presto.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)

Proper citation: ENDOG (RRID:SCR_013289) 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