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http://www.stat.washington.edu/thompson/Genepi/Eclipse.shtml

A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software)

Proper citation: ECLIPSE (RRID:SCR_013130) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/GRR/

A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)

Proper citation: GRR (RRID:SCR_013496) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Pedfiddler.shtml

Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)

Proper citation: PEDFIDDLER (RRID:SCR_013376) Copy   

•   Source: SciCrunch Registry

http://pga.gs.washington.edu/VG2.html

Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)

Proper citation: VG (RRID:SCR_013378) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/tagIMPUTE/

A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)

Proper citation: TAGIMPUTE (RRID:SCR_013338) Copy   

•   Source: SciCrunch Registry

http://www.dynacom.co.jp/u-tokyo.ac.jp/snphitlink/

Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)

Proper citation: SNP HITLINK (RRID:SCR_013340) Copy   

•   Source: SciCrunch Registry

http://software.bfh-inst2.de/download3.html

Software application (entry from Genetic Analysis Software)

Proper citation: SGS (RRID:SCR_013460) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Mcleeps.shtml

Software application (entry from Genetic Analysis Software)

Proper citation: MCLEEPS (RRID:SCR_013062) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/autoscan/

A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)

Proper citation: AUTOSCAN (RRID:SCR_013510) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/mmrrc/

Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability.

Proper citation: Mutant Mouse Resource and Research Center - Jackson Laboratory (RRID:SCR_016446) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/dna-microarray-core-facility-ualbany

Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments.

Proper citation: University at Albany Center for Functional Genomics DNA Microarray Core Facility (RRID:SCR_012502) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/gene-transfer-targeting-and-therapeutics-core/

Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates.

Proper citation: Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility (RRID:SCR_014847) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/functional-genomics/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5,2024.Core facility that provides Salk researchers access to gene expression analysis services such as whole-genome expression and genotyping using Affymetrix GeneChip technology, high-throughput qPCR and SNP services using Fluidigm Biomark System and Applied Biosystems 7900HT System, and DNA miniprep extraction using Qiagen BioRobot.

Proper citation: Salk Institute Functional Genomics Core Facility (RRID:SCR_014841) Copy   

•   Source: SciCrunch Registry

https://ccb-compute.cs.uni-saarland.de/mirtargetlink2/

Web application provides users with visualization interface to explore and analyze interaction networks between miRNAs and target genes.

Proper citation: miRTargetLink (RRID:SCR_026858) Copy   

•   Source: SciCrunch Registry

https://www.pharmaron.com/

Contract Research, Development, and Manufacturing Organization (CRDMO) supporting the life sciences industry. Founded in 2004, it provides comprehensive services for small molecules, biologics, and cell and gene therapies (CGT) from discovery to commercialization. Offers integrated R&D, laboratory services, and manufacturing.

Proper citation: Pharmaron (RRID:SCR_028035) Copy   

•   Source: SciCrunch Registry