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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   

•   Source: SciCrunch Registry

http://www.med.umich.edu/mgpc/

Center whose goal is to investigate signal transduction mechanisms regulating homeostasis and GI disorders. Their approach includes studies on genetics and gene regulation, cellular signaling pathways, receptors and ion channels.

Proper citation: University of Michigan Center for Gastrointestinal Research (RRID:SCR_015605) Copy   

•   Source: SciCrunch Registry

http://rc2resource.scripps.edu

Database portal for a project that aims to discover and characterize new molecular pathways that can be targeted pharmacologically to revert obesity-linked adipocyte defects that drive systemic insulin resistance and type 2 diabetes. It works to identify in tandem physiologically-relevant proteins and chemical tools in order to expedite their functional annotation and therapeutic validation.

Proper citation: Chemoproteomic identification and therapeutic validation of proteins of metabolic significance (RRID:SCR_015847) Copy   

•   Source: SciCrunch Registry

http://monogenicdiabetes.uchicago.edu/mody-registry-2/

Research project that aims to learn more about the number of people who have monogenic diabetes, why and how it happens, and how best to treat it. Any adult or child with a known genetic cause of diabetes may join the MODY Registry.

Proper citation: Monogenic Diabetes Registry (RRID:SCR_015883) Copy   

•   Source: SciCrunch Registry

http://www.ngsp.org

Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes.

Proper citation: National Glycohemoglobin Standardization Program (RRID:SCR_015885) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://plusconsortium.umn.edu

Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.

Proper citation: Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) Copy   

•   Source: SciCrunch Registry

https://kpmp.org

Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.

Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy   

•   Source: SciCrunch Registry

https://picrust.github.io/picrust/

Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.

Proper citation: PICRUSt (RRID:SCR_016855) Copy   

•   Source: SciCrunch Registry

http://zhoulab.usc.edu/TopDom/

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TopDom (RRID:SCR_016964) Copy   

•   Source: SciCrunch Registry

https://immunedb.readthedocs.io/en/latest/

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

Proper citation: ImmuneDB (RRID:SCR_017125) Copy   

•   Source: SciCrunch Registry

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301786/

Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing.

Proper citation: Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) 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://maayanlab.cloud/sigcom-lincs

Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.

Proper citation: SigCom LINCS (RRID:SCR_022275) Copy   

•   Source: SciCrunch Registry

https://github.com/zdk123/SpiecEasi

Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.

Proper citation: SpiecEasi (RRID:SCR_022712) Copy   

•   Source: SciCrunch Registry

https://huttenhower.sph.harvard.edu/picrust/

Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.

Proper citation: PICRUSt2 (RRID:SCR_022647) Copy   

•   Source: SciCrunch Registry

https://medschool.cuanschutz.edu/diabetes-research-center

Center to facilitate diabetes research at University of Colorado by integrating interdisciplinary basic, translational, and clinical diabetes research base; providing infrastructure and resources that are indispensable for continued discovery and progress towards diabetes research and developing improved prediction and disease prevention;providing P&F and enrichment programs to support DRC investigators and their trainees, and recruit new and young investigators into diabetes research.

Proper citation: University of Colorado Diabetes Research Center (RRID:SCR_022897) Copy   

•   Source: SciCrunch Registry

https://ncdiabetesresearch.org/

Interactive regional diabetes research community across four premiere research institutions in North Carolina, who currently garner over $70 million annually for support of their diabetes research: Duke University (Duke), The University of North Carolina at Chapel Hill (UNC), Wake Forest School of Medicine (WF), and North Carolina A&T State University (NC A&T State). NCDRC supports Research Cores that represent unique strengths at each institution.

Proper citation: North Carolina Diabetes Research Center (RRID:SCR_022896) Copy   

•   Source: SciCrunch Registry