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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Core facilitates access and usage of tissues and services to meet specialized needs of diabetes research community to expedite and catalyze innovative diabetes research at UC AMC. Provides resources to assist DRC investigators with acquisition and processing of rodent and human tissue, and specialized cell lines that are broadly required for diabetes research.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Tissue Procurement and Processing Core Facility (RRID:SCR_022904) Copy
Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip.
Proper citation: University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy (RRID:SCR_022740) Copy
https://labnodes.vanderbilt.edu/community/profile/id/1133
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides training and expertise in nutrition/diet methodology to obtain valid and reliable assessment and analyses of dietary intakes, nutritional status, body composition and metabolism.
Proper citation: Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core Facility (RRID:SCR_010191) Copy
https://www.bioconductor.org/packages/release/bioc/html/HiCDCPlus.html
Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP
Proper citation: HiCDCPlus (RRID:SCR_025317) Copy
Data visualization portal for HumanIslets project. Integrated platform for human islet data access and analysis. Includes data on human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at donor, islet and single-cell levels. Provides set of resources and tools to support metabolism and diabetes research community.
Proper citation: HumanIslets (RRID:SCR_025719) Copy
https://bioconductor.org/packages/release/bioc/html/trackViewer.html
Software R package to visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Proper citation: trackViewer (RRID:SCR_027743) Copy
https://github.com/VincentGardeux/demuxlet?tab=readme-ov-file
Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq.
Proper citation: demuxlet (RRID:SCR_027855) Copy
Centralized knowledge base of the human pancreas for diabetes research. Integrates diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be repository for reproducible, collaborative research within the pancreas and T1D realms.
Proper citation: PanKbase (RRID:SCR_026593) Copy
https://github.com/williamslab/ped-sim
Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.
Proper citation: ped-sim (RRID:SCR_026957) Copy
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