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https://github.com/qianli10000/mtradeR
Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.
Proper citation: mtradeR (RRID:SCR_022977) Copy
https://github.com/aametwally/Metabolic_Subphenotype_Predictor
Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes.
Proper citation: Metabolic Subphenotype Predictor (RRID:SCR_027192) Copy
https://github.com/SciCrunch/Antibody-Watch
Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research.
Proper citation: Antibody Watch (RRID:SCR_027424) Copy
Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.
Proper citation: Diabetic Complications Consortium (RRID:SCR_001415) Copy
Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families.
Proper citation: Pancreatlas (RRID:SCR_018567) Copy
https://gitlab.com/rosen-lab/white-adipose-atlas
Single cell atlas of human and mouse white adipose tissue.
Proper citation: White Adipose Atlas (RRID:SCR_023625) Copy
Ratings or validation data are available for this resource
https://github.com/BodenmillerGroup/imctools
Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.
Proper citation: imctools (RRID:SCR_017132) Copy
https://github.com/caleblareau/mgatk
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Proper citation: mgatk (RRID:SCR_021159) Copy
http://www2.niddk.nih.gov/Research/Resources/ObesityResources.htm
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 23, 2017. This website contains resources for obesity researchers including: Obesity Databases, Registries and Information; Obesity Multicenter Clinical Research; Obesity Basic Research Networks; Obesity Reagents; Obesity Services; Obesity Standardization Programs; Obesity Tissues, Cells, Animals; Obesity Useful Tools.
Proper citation: NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources (RRID:SCR_003074) Copy
University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.
Proper citation: Stanford Diabetes Research Center (RRID:SCR_015856) Copy
Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.
Proper citation: Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) Copy
Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes.
Proper citation: Clinical Islet Transplantation Consortium (CITC) (RRID:SCR_014385) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).
Proper citation: dkCOIN (RRID:SCR_004438) Copy
ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis.
Proper citation: ToppGene Suite (RRID:SCR_005726) Copy
https://github.com/vlink/marge
Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Proper citation: ToppCluster (RRID:SCR_001503) Copy
http://www.digestive.niddk.nih.gov
Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about digestive diseases among people with these conditions and their families, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NDDIC works closely with a coordinating panel of representatives from Federal agencies, voluntary organizations on the national level, and professional groups to identify and respond to informational needs about digestive diseases. NDDIC provides the following informational products and services: * Response to inquiries about digestive diseases - ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about specific digestive diseases, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. NDDIC also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine''''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to digestive diseases, as well as cross-cutting professional meetings. NDDIC exhibits at nine professional meetings each year, including Digestive Diseases Week, American College of Gastroenterology, Society of Gastroenterology Nurses and Associates, American Academy of Family Physicians, American Academy of Physician Assistants, American Nurses Association, and the National Conference for Nurse Practitioners.
Proper citation: National Digestive Diseases Information Clearinghouse (RRID:SCR_006771) Copy
Ratings or validation data are available for this resource
http://iidp.coh.org/Default.aspx
The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine.
Proper citation: Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) Copy
http://www.diabetes-translation.org
Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research.
Proper citation: Centers for Diabetes Translation Research (RRID:SCR_015149) Copy
http://globalprojects.ucsf.edu/project/novel-small-molecule-therapies-cystic-fibrosis
Research center that focuses on developing novel therapies for cystic fibrosis, enhancing research projects examining the mechanisms of the disease, and developing new small-molecule therapies that can be translated into the clinic.
Proper citation: Cystic Fibrosis Center - University of California San Francisco (RRID:SCR_015398) Copy
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