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http://bioconductor.org/packages/CATALYST/

Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.

Proper citation: CATALYST (RRID:SCR_017127) Copy   

•   Source: SciCrunch Registry

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry

http://grantome.com/grant/NIH/U01-DK099919-04S1

Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium.

Proper citation: Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://toppcluster.cchmc.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.signalingpathways.org/ominer/query.jsf

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).

Proper citation: Nuclear Receptor Signaling Atlas (RRID:SCR_003287) Copy   

•   Source: SciCrunch Registry

http://www.cristudy.org/Chronic-Kidney-Disease/Chronic-Renal-Insufficiency-Cohort-Study/

A prospective observational national cohort study poised to make fundamental insights into the epidemiology, management, and outcomes of chronic kidney disease (CKD) in adults with intended long-term follow up. The major goals of the CRIC Study are to answer two important questions: * Why does kidney disease get worse in some people, but not in others? * Why do persons with kidney disease commonly experience heart disease and stroke? The CRIC Scientific and Data Coordinating Center at Penn receives data and provides ongoing support for a number of Ancillary Studies approved by the CRIC Cohort utilizing both data collected about CRIC study participants as well as their biological samples. The CRIC Study has enrolled over 3900 men and women with CKD from 13 recruitment sites throughout the country. Following this group of individuals over the past 10 years has contributed to the knowledge of kidney disease, its treatment, and preventing its complications. The NIDDKwill be extending the study for an additional 5 years, through 2018. An extensive set of study data is collected from CRIC Study participants. With varying frequency, data are collected in the domains of medical history, physical measures, psychometrics and behaviors, biomarkers, genomics/metabolomics, as well as renal, cardiovascular and other outcomes. Measurements include creatinine clearance and iothalamate measured glomerular filtration rate. Cardiovascular measures include blood pressure, ECG, ABI, ECHO, and EBCT. Clinical CV outcomes include MI, ischemic heart disease-related death, acute coronary syndromes, congestive heart failure, cerebrovascular disease, peripheral vascular disease, and composite outcomes. The CRIC Study has delivered in excess of 150,000 bio-samples and a dataset characterizing all 3939 CRIC participants at the time of study entry to the NIDDKnational repository. The CRIC Study will also be delivering a dataset to NCBI''''s Database for Genotypes and Phenotypes.

Proper citation: Chronic Renal Insufficiency Cohort Study (RRID:SCR_009016) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/cgibd/cores/biostatistics

Core facility that provides comprehensive statistical and data management services. Its statistical analysis services include study design, power and sample size analysis, randomization, statistical programming, consultation and the development of analysis plans, graphs, figures and reports.

Proper citation: University of North Carolina Center for Gastrointestinal Biology and Disease Biostatistics and Data Management Core (RRID:SCR_015616) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/cgibd/cores/histology

Core facility that provides a full range of histology services, encompassing routine and specialized grossing, tissue processing, paraffin embedding, microtomy, H&E and special staining, and immunohistochemistry. It also offers image analysis and consultations to CGIBD members and non-members.

Proper citation: University of North Carolina Center for Gastrointestinal Biology and Disease Histology Core (RRID:SCR_015614) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/molecular/core_morphology.shtml

Core facility that provides histological services, equipment usage, and technical expertise to digestive and liver research projects.

Proper citation: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core (RRID:SCR_015618) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/molecular/core_molecular.shtml

Core facility that provides services that will enhance the analysis of both host and microbial biological processes as well as facilitate translation into the clinical arena via human subject research.

Proper citation: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core (RRID:SCR_015620) Copy   

•   Source: SciCrunch Registry

https://hddc.hms.harvard.edu/epithelial-cell-and-mucosal-immunology

Core facility that provides the infrastructure, biologic resources, expertise, and training for cross-disciplinary research on epithelial biology and immune function in mucosal surfaces and solid organs of the GI tract.

Proper citation: Harvard Digestive Diseases Center Biomedical CORE C: Epithelial Cell and Mucosal Immunology (RRID:SCR_015588) Copy   

•   Source: SciCrunch Registry

http://vmmpc.org/body-weight-regulation-core/

Core facility for MMPC Vanderbilt University School of Medicine for studying impact of genetic, surgical, dietary and pharmacologic manipulations on body weight regulation. Core provides measurement of food intake, energy expenditure, and behavioral factors. Energy balance studies are performed in mouse home cage to minimize stress. Mitochondrial function is assessed on permeabilized tissues, isolated cells, or isolated mitochondria. Mouse models of bariatric surgery have been developed and studied extensively.

Proper citation: MMPC Vanderbilt University School of Medicine Body Weight Regulation Core (RRID:SCR_015905) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu/immunology-core

Core that takes advantage of local expertise and resources to enable Center members to analyze cell populations in mouse or human livers. It performs complex analyses on small numbers of human cells, such as those obtained from liver biopsies.

Proper citation: UCSF Liver Center Immunology Core (RRID:SCR_015596) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu/clinical-translational-core

Core that supports study design to sample procurement and storage, to data analysis and presentation, and also focuses on research involving human subjects.

Proper citation: UCSF Liver Center Clinical & Translational Core (RRID:SCR_015598) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu/pathology-imaging-core

Core that provides services from routine liver histology to complex microscopy and image analysis.

Proper citation: UCSF Liver Center Pathology & Imaging Core (RRID:SCR_015599) Copy   

•   Source: SciCrunch Registry

https://hddc.hms.harvard.edu/clinical-translational-research-program

Core facility that supports basic, translational, and clinical research in the digestive diseases by providing access to human materials and resources in statistics and study design. Its services promote translation of basic research advances into improved clinical care by offering fresh and archived human specimens, associated clinical metadata, biostatistics and aid in study design.

Proper citation: Harvard Digestive Diseases Center Clinical Translational Research Program (RRID:SCR_015592) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/administrative-core

Core that has oversight of the other four cores of University of Chicago's Digestive Disease Research Core Center and determines the center's overall direction.

Proper citation: University of Chicago Digestive Diseases Research Core Center Administrative Core (RRID:SCR_015602) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/host-microbe-core

Core that consists of two components: The Enteric Microbiology and The Gnotobiotic Mouse components. The Enteric Microbiology component offers novel screening and advanced technologies for compositional and functional profiling of the resident microbial communities in the gastrointestinal tract. The Gnotobiotic Mouse component enables investigators to study the effects and causal role of specific microorganisms or profiles in vivo.

Proper citation: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core (RRID:SCR_015603) Copy   

•   Source: SciCrunch Registry