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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SCDE Resource Report Resource Website 10+ mentions |
SCDE (RRID:SCR_015952) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.) | statistic, single, cell, rna, seq, rnaseq, differential, analysis, pathway, gene, geneset, dispersion, overdispersion, bayesian, expression, magnitude | Leukemia and Lymphoma Research UK ; Leukemia and Lymphoma Society ; NHLBI R01 HL097794; NIA K25 AG037596; NIDDK R01 DK050234 |
PMID:24836921 | Free, Available for download | SCR_015952 | 2026-09-19 12:55:15 | 32 | |||||||||
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APA-Scan Resource Report Resource Website |
APA-Scan (RRID:SCR_022974) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data. | annotated and potential alternative polyadenylation events, gene downstream 3'-UTR, RNA-seq and 3'-end-seq data, two different biological conditions, polyadenylation events | NIDDK DK097771; NIGMS R01GM113952; NSF FET2003749 |
PMID:36171568 | Free, Available for download, Freely available | SCR_022974 | 2026-09-19 12:55:26 | 0 | |||||||||
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Mouse Mutagenesis Center for Developmental Defects Resource Report Resource Website |
Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) | Mouse Mutagenesis for Developmental Defects | material resource, reagent supplier | THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval. | mutant, embryo, post embryonic, mutagenesis, craniofacial, eye, fertility, growth, lethal, metabolism, neurological, skeletal, skin, coat, urogenital, cryopreserved, enu, defect, birth defect, , patterning defect, growth defect, endocrine defects, neurological anomaly, blood defect, mouse model, human disease, n-ethyl-n-nitrosourea, chromosome 11, phenotype |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mutant Mouse Resource and Research Center is related to: Jackson Laboratory has parent organization: Baylor University; Texas; USA |
Aging | NICHD ; NIGMS ; NIA ; NIAMS ; NHLBI ; NIDDK ; NIDCR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00190 | SCR_007321 | NIH Mouse Mutagenesis Center for Developmental Defects | 2026-09-19 12:55:57 | 0 | |||||
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Pediatric Obesity Microbiome and Metabolism Study Resource Report Resource Website 1+ mentions |
Pediatric Obesity Microbiome and Metabolism Study (RRID:SCR_021071) | POMMS | biospecimen repository, data or information resource, disease-related portal, material storage repository, portal, service resource, storage service resource, topical portal | Biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Biorepository is available as shared resource. | Gut microbiome analysis, marker gene, shotgun DNA sequencing, clinical data, metabolomic data, microbiome samples, biorespository, adolescent obesity |
has parent organization: Duke University; North Carolina; USA has parent organization: Northwestern University; Illinois; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Obesity | NIDDK R24 DK110492 | DOI:10.1002/oby.23081 | Free, Freely available | SCR_021071 | 2026-09-19 12:54:48 | 1 | ||||||
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sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data analysis software, data processing software, software application, software resource | 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. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NHGRI R01 HG006129; NIDDK R01 DK094699 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | 2026-09-19 12:53:30 | 28 | ||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 10+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | catalog, data or information resource, database, portal, project portal | 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. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIDDK ; NIH |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-09-19 12:53:30 | 11 | ||||||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | 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. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-09-19 12:53:32 | 5 | |||||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; NIH Office Of The Director S10 OD016350 |
PMID:29491378 | SCR_017129 | 2026-09-19 12:53:34 | 1 | |||||||||
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CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | data access protocol, data analysis software, data processing software, software application, software resource, web service | Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability. | classify, sort, single, cell, mass, cytometry, data, cycle, state, volume, heterogeneity, quantify, volume, variability | European Research Council ; NIDDK UC4 DK108132; SNSF ; SystemsX MetastasiX grant |
PMID:29434325 | Free, Restricted | SCR_017128 | 2026-09-19 12:53:34 | 0 | |||||||||
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Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions Resource Report Resource Website |
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) | HIBACHI, hibachi | simulation software, software application, software resource | Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods. | data, simulation, dataset, compare, machine, evaluate, learning, method | NIAID AI116794; NIDDK DK112217; NLM LM012601 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-09-19 12:53:35 | 0 | |||||||
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HIRN Consortium on Modeling Autoimmune Interactions Resource Report Resource Website 1+ mentions |
HIRN Consortium on Modeling Autoimmune Interactions (RRID:SCR_016200) | HIRN-CMAI | consortium, data or information resource, organization portal, portal | 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. | autoimmune, disease, immunobiology, in vitro, research, in vivo | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK U01 DK107383; NIDDK UC4 DK104194; NIDDK UC4 DK104207; NIDDK UC4 DK104218; NIDDK UC4 DK104223; NIDDK UC4 DK116284 |
SCR_016200 | Consortium on Modeling Autoimmune Interactions (HIRN-CMAI) | 2026-09-19 12:53:19 | 1 | ||||||||
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HIRN Bioinformatics Center Resource Report Resource Website 1+ mentions |
HIRN Bioinformatics Center (RRID:SCR_016203) | HIRN-BC | consortium, data or information resource, organization portal, portal | 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). | bioinformatics, sharing, maintenance, data set, bioengineering | is organization facet of: Human Islet Research Network (HIRN) | Type 1 diabetes, Diabetes | NIDDK ; NIDDK U01 DK104147 |
http://bclabs.hirnetwork.org/ | SCR_016203 | 2026-09-19 12:53:19 | 1 | |||||||
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Diabetes Epigenome Atlas Resource Report Resource Website 1+ mentions |
Diabetes Epigenome Atlas (RRID:SCR_016441) | atlas, data or information resource, database, disease-related portal, portal, topical portal | 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. | collect, provide, data, human, genome, epigenome, genetic, study, type 2 diabetes |
has parent organization: Stanford University; Stanford; California has parent organization: University of California at San Diego; California; USA |
type 2 diabetes | NIDDK U01 DK100554 | Free, Proprietary data are available only to approved AMP consortium users with user accounts | SCR_016537 | SCR_016441 | 2026-09-19 12:53:23 | 2 | |||||||
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biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data analysis software, data processing software, software application, software resource, software toolkit | 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. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
ARO W911NF1110473; NHGRI R01 HG005220; NHGRI R01 HG005969; NIDDK U54 DE023798; NSF DBI1053486; Sloan Foundation 4406J0B |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | bioBakery, biobakery | 2026-09-19 12:53:26 | 18 | |||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | data analysis software, data processing software, software application, software resource | 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. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI F32CA165823; NCI K12 CA139160; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595; NIGMS U01 GM092691; NIGMS U01 GM61393; NIMH P50 MH094267; NIMH R01 MH090937; NIMH R01 MH101820; NIMH T32 MH020065 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-09-19 12:53:28 | 25 | |||||||||
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Michigan Center for Diabetes Translational Research Resource Report Resource Website 1+ mentions |
Michigan Center for Diabetes Translational Research (RRID:SCR_015187) | MCDTR | data or information resource, disease-related portal, portal, topical portal | Multidisciplinary unit of the University of Michigan funded by National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health. MCDTR is one of seven NIH Centers funded to focus on type 2 translational research in diabetes with mission to establish, promote, and enhance multidisciplinary collaboration among researchers directed at prevention and control of diabetes, its complications, and comorbidities, by providing access to specialized expertise and resources. | translational diabetes research, multidisciplinary collabroation, clinical research, implementation research |
is affiliated with: Centers for Diabetes Translation Research has parent organization: University of Michigan Medical School; Michigan; USA is parent organization of: Michigan Center for Diabetes Translational Research Administrative Core Facility is parent organization of: Michigan Center for Diabetes Translational Research Methods and Measurements Core is parent organization of: Michigan Center for Diabetes Translational Research Intervention and Technology Research Core is parent organization of: Michigan Center for Diabetes Translational Research Leveraging Community, Peer, and Family Support Core Facility has organization facet: Michigan Center for Diabetes Translational Research Administrative Core Facility has organization facet: Michigan Center for Diabetes Translational Research Methods and Measurements Core has organization facet: Michigan Center for Diabetes Translational Research Intervention and Technology Research Core has organization facet: Michigan Center for Diabetes Translational Research Leveraging Community, Peer, and Family Support Core Facility is organization facet of: Centers for Diabetes Translation Research |
Diabetes | NIDDK P30DK092926 | http://diabetesresearch.med.umich.edu | SCR_015187 | 2026-09-19 12:53:06 | 1 | |||||||
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Center for Iron and Heme Disorders at the University of Utah Resource Report Resource Website |
Center for Iron and Heme Disorders at the University of Utah (RRID:SCR_015341) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical portal | Research center for iron and hematology research. It hosts cores that provide services for mutation generation and detection, metabolomics, and iron and heme experiments and research. In addition to these cores, it has an Enrichment Program, and Internal and External Advisory Committees, and a Pilot and Feasibility program. | iron and hematology research, mutation generation, metabolomics, enrichment progarm. |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Utah School of Medicine; Utah; USA is parent organization of: Center for Iron and Heme Disorders at the University of Utah Administrative Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Metabolomics Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Metabolomics Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Administrative Core is organization facet of: Hematology Centers |
iron disorder, heme disorder | NIDDK U54DK110858 | Available to the research community | SCR_015341 | 2026-09-19 12:53:07 | 0 | ||||||||
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University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Resource Report Resource Website |
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center (RRID:SCR_015462) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical portal | Center whose goals include providing resources and support to investigators conducting multidisciplinary and interdisciplinary research in nutritional sciences and obesity, strengthening clinical nutrition training programs for medical students, practicing physicians, and allied health personnel, and translating findings from obesity and nutrition research to the general public. | obesity research center, nutritional sciences, obesity research |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Research Facilitation Program is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Biostatistics Program is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Animal Metabolism Phenotyping Core is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Metabolic Molecular Phenotyping Core is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Communication for Health Applications and Interventions Core is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Clinical Nutrition Research Facilitation Program is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core is parent organization of: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Diet and Physical Activity Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Diet and Physical Activity Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Metabolic Molecular Phenotyping Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Communication for Health Applications and Interventions Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Animal Metabolism Phenotyping Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Nutrigenetics Core has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Biostatistics Program has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Clinical Nutrition Research Facilitation Program has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Research Facilitation Program is organization facet of: Nutrition and Obesity Research Centers |
Obesity | NIDDK DK056350 | Available to the research community | SCR_015462 | 2026-09-19 12:53:08 | 0 | ||||||||
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Vanderbilt Digestive Disease Research Center Resource Report Resource Website |
Vanderbilt Digestive Disease Research Center (RRID:SCR_015225) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical portal | Center whose objectives include promoting digestive diseases-related research in an integrative, collaborative and multidisciplinary manner, developing and implementing programs for attracting, training, and retaining young investigators in digestive disease-related research, and facilitating the transfer of basic research discoveries to improvements in prevention and/or clinical care. | digestive diseases, clinical research |
is listed by: NIDDK Information Network (dkNET) has parent organization: Vanderbilt University Medical Center; Tennessee; USA is parent organization of: Vanderbilt Digestive Disease Research Center Flow Cytometry Core is parent organization of: Vanderbilt Digestive Disease Research Center Cellular Imaging Core is parent organization of: Vanderbilt Digestive Disease Research Center Bioanalytical Mass Spectrometry and Proteomics Core has organization facet: Vanderbilt Digestive Disease Research Center Bioanalytical Mass Spectrometry and Proteomics Core has organization facet: Vanderbilt Digestive Disease Research Center Cellular Imaging Core has organization facet: Vanderbilt Digestive Disease Research Center Flow Cytometry Core has organization facet: Vanderbilt Digestive Disease Research Center Biostatistics Administrative Core is organization facet of: Digestive Disease Centers |
digestive disease | NIDDK DK058404 | Available to the research community | SCR_015225 | 2026-09-19 12:53:06 | 0 | ||||||||
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University of Washington Nutrition and Obesity Research Center Resource Report Resource Website |
University of Washington Nutrition and Obesity Research Center (RRID:SCR_015475) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical portal | Research center that facilitates the integration and coordination of the ongoing activities of the University of Washington system. Its overarching goals are to foster interdisciplinary research collaborations, stimulate new research activities, improve nutrition and obesity education, and facilitate optimal nutritional management of patients. | nutrition research center, obesity research center, nutritional management |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Washington; Seattle; USA is parent organization of: University of Washington Nutrition and Obesity Research Center Adipose Tissue and Obesity Core is parent organization of: University of Washington Nutrition and Obesity Research Center Administrative and Enrichment Core is parent organization of: University of Washington Nutrition and Obesity Research Center Analytic Core is parent organization of: University of Washington Nutrition and Obesity Research Center Energy Balance Core has organization facet: University of Washington Nutrition and Obesity Research Center Energy Balance Core has organization facet: University of Washington Nutrition and Obesity Research Center Adipose Tissue and Obesity Core has organization facet: University of Washington Nutrition and Obesity Research Center Analytic Core has organization facet: University of Washington Nutrition and Obesity Research Center Administrative and Enrichment Core is organization facet of: Nutrition and Obesity Research Centers |
Obesity | NIDDK P30DK035816 | Available to the research community, Acknowledgement requested | SCR_015475 | 2026-09-19 12:53:08 | 0 |
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