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https://assess-aki.hmc.psu.edu/

A study which recruits patients with and without an episode of acute kidney injury during a hospitalization, and follows them longitudinally for major cardiac, renal and mortality events. An important aspect of the study is the prospective evaluation of potential biomarkers for renal and cardiac outcomes.

Proper citation: Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) (RRID:SCR_014386) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu

Center whose goal is to integrate bench science with clinical investigation, in support of its vision to understand and cure human liver diseases.

Proper citation: UCSF Liver Center (RRID:SCR_015595) Copy   

•   Source: SciCrunch Registry

http://www.d2dstudy.org/

A study to determine whether vitamin D supplementation is safe and effective in delaying the onset of type 2 diabetes in people at risk for the disease and to gain a better understanding of how vitamin D affects glucose metabolism.

Proper citation: Vitamin D to Prevent Type 2 Diabetes (D2d) (RRID:SCR_014382) Copy   

•   Source: SciCrunch Registry

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

Core facility that maintains a centralized repository of cells and reagents pertinent to digestive, liver and pancreatic disease research. It also provides training for labs in new cell culture (2D and 3D) techniques.

Proper citation: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core (RRID:SCR_015621) Copy   

•   Source: SciCrunch Registry

http://livercenter.ucsf.edu/cell-biology-core

Core whose purpose is providing primary and immortalized liver cells for experimental use as well as other material such as human liver cells, primary hepatocytes, and immortalized cell lines.

Proper citation: UCSF Liver Center Cell Biology Core (RRID:SCR_015600) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org/research-cores/integrated-translational-research-core

Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research.

Proper citation: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core (RRID:SCR_015606) Copy   

•   Source: SciCrunch Registry

https://cran.rstudio.com/web/packages/accucor/index.html

Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data.

Proper citation: AccuCor (RRID:SCR_023046) Copy   

•   Source: SciCrunch Registry

http://secrepedia.org

Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease.

Proper citation: Secrepedia (RRID:SCR_022590) Copy   

•   Source: SciCrunch Registry

http://hms-dbmi.github.io/scde/index.html

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.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/APA-Scan

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.

Proper citation: APA-Scan (RRID:SCR_022974) Copy   

•   Source: SciCrunch Registry

https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4

Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.

Proper citation: GeneRanger (RRID:SCR_023622) Copy   

•   Source: SciCrunch Registry

https://targetranger.maayanlab.cloud/

Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.

Proper citation: TargetRanger (RRID:SCR_023621) Copy   

•   Source: SciCrunch Registry

https://www.medibeacon.com/science/preclinical/

Transdermal Glomerular Filtration Rate monitor used to assess renal function in mouse and rat models of acute kidney injury and chronic kidney disease.

Proper citation: MediBeacon: Transdermal GFR Monitor (RRID:SCR_024533) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionalUrology/SpheroScan

Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results.

Proper citation: SpheroScan (RRID:SCR_023886) Copy   

•   Source: SciCrunch Registry

https://github.com/kwanjeeraw/metabox

Software R toolbox for thorough metabolomic data analysis, integration and interpretation. Metabox 2.0 is updated version of R package Metabox and includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation.

Proper citation: Metabox (RRID:SCR_024443) Copy   

•   Source: SciCrunch Registry

http://www.childrennetwork.org/

Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study.

Proper citation: Childhood Liver Disease Research and Education Network (RRID:SCR_001497) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://norccentral.org

Portal to research centers and core facilities specifically support obesity research and better understand the relationship between health and nutrition.

Proper citation: Nutrition and Obesity Research Centers (RRID:SCR_004131) Copy   

•   Source: SciCrunch Registry

http://www.ndriresource.org/NDRI_Initiatives/HBDI/36/

Database of medical history and genealogical data on over 6700 families who are affected by type 1 diabetes and a repository of DNA and immortalized cell lines collected from 500 families. This database and repository was originally created to help researchers uncover the genetic causes of type 1 diabetes but today, it is also used by researchers who study type 2 diabetes, diabetic complications, autoimmune diseases, kidney disease, and other disorders. The following resources and services are available to researchers through HBDI: * International Type 1 Diabetes Database: This database includes more than 6700 families with diabetes, related complications and other genetic diseases. There are extensive genealogical and medical histories for more than 90,000 individuals. NDRI conducts searches of the database for approved research requests. * HBDI Catalog: The catalog contains 503 family pedigrees with associated cell lines, DNA, and serum for research. Also available are HLA-typing and auto-antibody test results for diabetes families in the catalog. * HBDI Repository: The HBDI repository contains cell lines, DNA, and HLA typing information from 480 families, and frozen buffy coats from 23 families, all with Type 1 diabetes. They have recently expanded the repository to include specimens from individuals with rare diseases. * Customized Collections: NDRI will collect data from patients and physicians, conduct phone interviews and collect blood and other specimens for research on request., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Human Biological Data Interchange (RRID:SCR_004591) Copy   

•   Source: SciCrunch Registry