Tools   Select Another Resource Report Type

https://sdrc.stanford.edu/sdrc-research-cores/sirc/home/

Core facility whose services include: Islet Isolation, Islet transplantation, Islet Culture, Islet Perifusion & Islet Hormone Assays. The SIRC is supported by the Stanford Diabetes Research Center (SDRC).

Proper citation: Stanford Diabetes Research Center Stanford Islet Research Core (RRID:SCR_016211) Copy   

•   Source: SciCrunch Registry
  

https://flow.ucsf.edu/

Core assists investigators whose research requires molecular marker characterization of cells in suspension as well as isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are provided.

Proper citation: University of California San Francisco Parnassus Flow Cytometry Core Facility (RRID:SCR_018206) Copy   

•   Source: SciCrunch Registry
  

https://matkp.org/

Open community portal for multi-species mammalian adipose biology. Aggregates data for adipose tissues and cell types, genes active within them, and their relationship to human phenotypes. Plans to offer reproducible analysis pipelines, wet lab and computational protocols, datasets, analyses, and visualizations for epigenomic, transcriptomic, proteomic, metabolomic, and imaging data. Designed to aggregate and harmonize multi-species (human and mouse) transcriptomic, genetic, and epigenomic data. Enables to explore adipose biology, cell-type-specific gene expression, and metabolic disease mechanisms through interactive tools like Single Cell Browsers.

Proper citation: Mammalian Adipose Tissue Knowledge Portal (RRID:SCR_028031) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cafferychen777/ggpicrust2

Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.

Proper citation: ggpicrust2 (RRID:SCR_025965) Copy   

•   Source: SciCrunch Registry
  

https://aireadi.org

Multidisciplinary data generation project which aims to create and share multimodal dataset optimized for artificial intelligence research in type 2 diabetes. At each release of the AI-READI dataset, two sets will be made available: public access and controlled access set. The public set will be stripped of Protected Health Information (PHI) as well as information related to the sex and race/ethnicity of the participants.

Proper citation: AI-READI (RRID:SCR_027031) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Danko-Lab/dREG

Software tool for detecting regulatory elements using GRO-seq and PRO-seq.

Proper citation: dREG (RRID:SCR_027012) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.chemperturbdb.com

Artificial Intelligence (AI)-powered website, which provides user-friendly open access analysis of extensive ChemPerturb-seq dataset.

Proper citation: ChemPerturbDB (RRID:SCR_027190) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/zeyang-shen/maggie

Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship.

Proper citation: Motif Alteration Genome wide to Globally Investigate Elements (RRID:SCR_021903) Copy   

•   Source: SciCrunch Registry
  

https://spin.niddk.nih.gov/bax/software/TALOS-N/

Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts.

Proper citation: TALOS-N (RRID:SCR_022800) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://ubbmc.buffalo.edu/research/ibsos.php

Multi-center placebo-controlled randomized clinical trial to assess the short-term and long-term efficacy of cognitive behavior therapy (CBT) for irritable bowel syndrome (IBS) using two treatment delivery systems: self administered CBT and therapist administered CBT. Long term project goals are to develop an effective self-administered behavioral treatment program that can enhance the quality of patient care, improve clinical outcomes, and decrease the economic and personal costs of one of the most prevalent and intractable gastrointestinal disorders.

Proper citation: Irritable Bowel Syndrome Outcome Study (RRID:SCR_001504) Copy   

•   Source: SciCrunch Registry
  

https://www.clinicaltrials.gov/study/NCT00064753

Multi-center, randomized, double blind controlled clinical trial to determine whether treatment with a standard multivitamin augmented with high doses of folic acid, vitamin B6 and vitamin B12 reduces the rate of cardiovascular disease outcomes in renal transplant recipients relative to participants receiving a similar multivitamin that contains no folic acid. This study hopes to show that by reducing the level of homocysteine in the body, the risk of heart disease is also reduced among kidney transplant patients.

Proper citation: Folic Acid for Vascular Outcome Reduction in Transplantation (RRID:SCR_001505) Copy   

•   Source: SciCrunch Registry
  

https://clinicaltrials.gov/study/NCT00342927?term=AREA%5BBasicSearch%5D(NIDDK%20endocrine%20and%20diabetes)%20AND%20AREA%5BSponsorSearch%5D(NIDDK)%20AND%20AREA%5BOverallStatus%5D(NOT_YET_RECRUITING%20OR%20RECRUITING%20OR%20ACTIVE_NOT_RECRUITING)&rank=1

Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease

Proper citation: Family Investigation of Nephropathy of Diabetes (RRID:SCR_001525) Copy   

•   Source: SciCrunch Registry
  

https://clinicaltrials.gov/study/NCT01885559

Consortium established to design and implement clinical trials of treatments that might slow the progressive loss of renal function in Polycystic Kidney Disease (PKD). Two multicenter randomized, double-blind, placebo controlled clinical trials are running concurrently to study the efficacy of renin-angiotensin-aldosterone system blockade on the progression of cystic disease (kidney volume) and on the decline in renal function in autosomal dominant polycystic kidney disease (ADPKD). Study A is to study whether intensive ACE-I/ARB blockade decrease the progression of cystic disease compared to ACE-I monotherapy patients with early disease, relatively preserved renal function, and high-normal BP or hypertension. Study B is to study whether intensive ACE-I/ARB blockade as compared to ACE-I monotherapy slow the decline in kidney function, end-stage of renal disease, or death in the setting of standard blood pressure control in hypertensive patients with moderately advanced disease.

Proper citation: HALT PKD (RRID:SCR_001529) Copy   

•   Source: SciCrunch Registry
  

http://www.isletstudy.org/

Network of centers to conduct studies of islet transplantation in patients with type 1 diabetes to improve the safety and long-term success of methods for transplanting islets. It is the aim of this trial to improve methods of isolating islets, to improve techniques for the administering those transplanted islets; and to develop approaches to minimize the toxic effects of immunosuppressive drugs required for transplantation.

Proper citation: Clinical Islet Transplantation Study (RRID:SCR_001515) Copy   

•   Source: SciCrunch Registry
  

https://sites.cscc.unc.edu/cscc/projects/RIVUR%20

Multicenter, randomized, double-blind, placebo-controlled trial is designed to determine whether daily antimicrobial prophylaxis is superior to placebo in preventing recurrence of urinary tract infection (UTI) in children with vesicoureteral reflux (VUR). The basic eligibility criteria are: (1) age at randomization of at least 2 months, but less than 6 years, (2) a diagnosed first febrile or symptomatic UTI within 42 days prior to randomization that was appropriately treated, and (3) presence of Grade I-IV VUR based on voiding cystourethrogram (VCUG). Patients will be randomly assigned to treatment for 2 years with daily antimicrobial prophylaxis (trimethoprim-sulfamethoxazole) or placebo. The study is designed to recruit 600 children (approximately 300 in each treatment group) over an 18-24 month period. The primary endpoint is recurrence of UTI. In addition, patients will be evaluated for secondary endpoints related to renal scarring and antimicrobial resistance. Scarring will be determined based on renal scintigraphy by 99mTc dimercaptosuccinic (DMSA) scan. Quality of life, compliance, safety parameters, utilization of health resources, and change in VUR will be assessed periodically throughout the study.

Proper citation: RiVuR (RRID:SCR_001539) Copy   

•   Source: SciCrunch Registry