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http://mouse.brain-map.org/static/atlas

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy   

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https://dgrc.bio.indiana.edu/Home

Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.

Proper citation: Drosophila Genomics Resource Center (RRID:SCR_002845) Copy   

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http://ccr.coriell.org/Sections/Collections/NHGRI/?SsId=11

DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.

Proper citation: NHGRI Sample Repository for Human Genetic Research (RRID:SCR_004528) Copy   

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http://www.cs.cmu.edu/~jernst/stem/

The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Short Time-series Expression Miner (STEM) (RRID:SCR_005016) Copy   

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http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

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http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

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http://www.ihwg.org/

The IHWG Cell and DNA Bank was established as a shared resource to support the scientific projects of the 13th International Histocompatibility Workshop (IHWS). The Research Cell Bank (RCB), located in Fred Hutchinson Cancer Research Center in Seattle, WA, maintains the IHWG inventory. This comprehensive inventory includes B-Lymphoblastoid Cell Lines (B-LCL) from previous International Workshops, HLA heterozygous and homozygous donors, selected families, and individuals of diverse population groups. The RCB maintains stocks of purified DNA derived from these cell lines, as well as DNA reference panels that provide an extensive array of HLA and HLA-related sequence polymorphisms. The RCB also provides cloned HLA genes and B-LCL transfected with selected HLA genes, which are available on a limited basis.

Proper citation: International Histocompatibility Cell and DNA Bank (RRID:SCR_004871) Copy   

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

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

Proper citation: LDHEATMAP (RRID:SCR_006312) Copy   

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http://www.ebi.ac.uk/Tools/blast2/index.html

It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes.

Proper citation: Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) Copy   

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http://www.gepas.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management.

Proper citation: Gene Expression Profile Analysis Suite (RRID:SCR_008341) Copy   

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

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

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https://bioconductor.org/packages/release/bioc/html/scran.html

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

Proper citation: scran (RRID:SCR_016944) Copy   

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https://github.com/ehodzic/cd-CAP

Software designed for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples.

Proper citation: cd-CAP software (RRID:SCR_016843) Copy   

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https://www.networkanalyst.ca/

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy   

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https://sourceforge.net/projects/jtreeview/

Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure.

Proper citation: Java Treeview (RRID:SCR_016916) Copy   

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https://pachterlab.github.io/sleuth/about

Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.

Proper citation: sleuth (RRID:SCR_016883) Copy   

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http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy   

•   Source: SciCrunch Registry

https://github.com/flo-compbio/xlmhg

Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment.

Proper citation: XL-mHG (RRID:SCR_016846) Copy   

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http://biotecnun.unav.es:8080/app/TranscriptAchilles

Software genome-wide tool to predict transcript biomarkers of gene essentiality in cancer. This tool can be used to predict new potential target genes with their corresponding biomarkers (either transcript or gene expression).

Proper citation: TranscriptAchilles (RRID:SCR_016849) Copy   

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https://github.com/maypoleflyn/BSATOS

Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.

Proper citation: Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) Copy   

•   Source: SciCrunch Registry