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A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.
Proper citation: CalR (RRID:SCR_015849) Copy
Biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Biorepository is available as shared resource.
Proper citation: Pediatric Obesity Microbiome and Metabolism Study (RRID:SCR_021071) Copy
https://crispresso.pinellolab.partners.org/submission
Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.
Proper citation: CRISPResso (RRID:SCR_021538) Copy
https://github.com/macs3-project/MACS
Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
Proper citation: MACS (RRID:SCR_013291) Copy
http://www.metabolomicsworkbench.org
Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.
Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy
https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.
Proper citation: Skyline (RRID:SCR_014080) Copy
https://hirnetwork.org/consortium/cmai
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms.
Proper citation: HIRN Consortium on Modeling Autoimmune Interactions (RRID:SCR_016200) Copy
https://hirnetwork.org/coordinating_group/hirec
The Bioinformatics Center is located within the Department of Diabetes and Cancer Discovery Science at City of Hope and was established in 2014 to support the Human Islet Research Network (HIRN). The overall objective of the Bioinformatics Center is to advance type 1 diabetes knowledge generated through HIRN by providing the bioinformatics capability and infrastructure needed to support the Network. To achieve this goal, the Bioinformatics Center provides investigators with tools, processes, and methods to facilitate long term sharing, maintenance, and management of HIRN developed resources, including datasets, technologies, documents, and bioreagents. Collaboration and communication are cultivated through consultation and outreach activities. In 2019, HIRN received funding to continue HIRN Coordinating Center (CC) and Bioinformatics Center (BC) as Human Islet Research Enhancement Center (HIREC).
Proper citation: HIRN Bioinformatics Center (RRID:SCR_016203) Copy
Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers.
Proper citation: Diabetes Epigenome Atlas (RRID:SCR_016441) Copy
https://bitbucket.org/biobakery/biobakery/wiki/Home
Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: biobakery (RRID:SCR_016596) Copy
https://github.com/hakyimlab/PrediXcan
Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.
Proper citation: PrediXcan (RRID:SCR_016739) Copy
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
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
https://www.sciencescott.com/pyminer
Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Proper citation: PyMINEr (RRID:SCR_016990) Copy
http://www.scandb.org/newinterface/about.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SCAN (RRID:SCR_005185) Copy
https://gataca.cchmc.org/gataca/gudmap
A database which can be used to search for genes critical for a variety of Genito-Urinary system functions and diseases.
Proper citation: GATACA GUDMAP Gene Explorer (RRID:SCR_014518) Copy
Program is performing deep phenotyping of human endocrine pancreas and its interaction with immune system to better understand cellular and molecular events that precede and lead to beta cell loss in Type-1 Diabetes (T1D) and islet dysfunction in Type-2 Diabetes (T2D).
Proper citation: HIRN Human Pancreas Analysis Program (RRID:SCR_016202) Copy
http://www.med.umich.edu/mgpc/cores/vivo.htm
Core facility that consists of the following 4 distinct programs: In Vivo Small Animal Studies Program, Organoid/Enteroid Modeling Program, Biospecimens Banking Service, and Clinical Design and Statistics.
Proper citation: University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core (RRID:SCR_015608) Copy
http://www.uchicagoddrcc.org/research-cores/tissue-and-cell-analysis-core
Core whose services include anatomic pathology review of human and experimental animal tissues as well as consultation in the best approaches for such analyses, cost-effective and high quality processing and staining of formalin-fixed paraffin-embedded tissues, and making collections of human tissue and imaging technologies available to researchers.
Proper citation: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core (RRID:SCR_015607) Copy
http://www.broadinstitute.org/pubs/MitoCarta/
Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.
Proper citation: MitoCarta (RRID:SCR_018165) Copy
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