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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
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
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
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
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
http://www.med.upenn.edu/idom/drc/cores/ria.html
Core which offers high quality immunoassay services to basic, translational, and clinical investigators performing diabetes and related metabolic disease research. The core also provides consultation and training and education services.
Proper citation: Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core Facility (RRID:SCR_010028) Copy
http://www.med.upenn.edu/gtp/vectorcore/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core whose main aim is to provide vector technology for preclinical studies and other basic research applications. Its services include rovision of AAV, adenoviral and lentiviral based vectors, consultation and advice in the design of custom vectors and in vector serotype/pseudotype selection, and design, cloning and production of plasmid DNA for the production of custom vectors.
Proper citation: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core Facility (RRID:SCR_010038) Copy
https://labnodes.vanderbilt.edu/community/profile/id/2230
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that supports diabetes, endocrine, and metabolic research across a range of species. Its objective is to provide sensitive, reproducible, and inexpensive analyses of hormones, amino acids, and other relevant chemicals.
Proper citation: Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core Facility (RRID:SCR_010181) Copy
https://labnodes.vanderbilt.edu/community/profile/id/2229
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides any Vanderbilt researcher with access to imaging equipment and expert technical support for microscopy and analysis of tissue and cellular physiology.
Proper citation: Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource Core Facility (RRID:SCR_010165) Copy
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
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
Artificial Intelligence (AI)-powered website, which provides user-friendly open access analysis of extensive ChemPerturb-seq dataset.
Proper citation: ChemPerturbDB (RRID:SCR_027190) Copy
Provides Cincinnati Children s Hospital Medical Center; Cincinnati; Ohio resources in confocal, wide-field, and spatial technique applications.
Proper citation: Cincinnati Children's Hospital Confocal Imaging Core Facility (RRID:SCR_022628) Copy
https://ncdiabetesresearch.org/acsmc
Core to leverage data, patient populations and investigators at each NCDRC institution, including accessing expertise and resources of regional Clinical and Translational Science Institute hubs (Duke, UNC, and Wake Forest). Research navigators in ACSMC provides input and navigation of clinical research resources available to diabetes investigators based on extensive experience in diabetes specific studies and methodology and deep knowledge of NCDRC resources available at each institution.
Proper citation: North Carolina Diabetes Research Center Advanced Clinical Study Methods Core Facility (RRID:SCR_022908) Copy
Provides diabetes researchers at University of Colorado with access to microscopy and mass cytometry systems. Provides expertise and training to use equipment effectively for diabetes related tissues; expertise and validated diabetes related resources to prepare samples appropriately; guidance to design experiments; resources to analyze data; assistance with data interpretation.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Cell and Tissue Analysis Core Facility (RRID:SCR_022906) Copy
Provides diabetes researchers with access to novel human stem cell-derived in vitro cell models for investigating cellular and molecular features of both Type 1 and Type 2 diabetes. Recent progress in stem cell, organoid culture, gene editing and directed differentiation technologies has afforded opportunities to develop pre-clinical human models.Provides expertise, infrastructure and access to novel human model systems and technologies to DRC investigators. Provides expertise, resources and training in stem cell technologies together with quality control testing, validation standardization and authentication all model platforms and reagents.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Disease Modeling Core Facility (RRID:SCR_022905) Copy
Core leverages current clinical research facilities and equipment available at Barbara Davis Center for Childhood Diabetes, UC AMC Clinical Translational Research Center, University of Colorado Hospital, Denver Veteran Administration Medical Center and Children Hospital Colorado.Core integrates diabetes research across these institutions through communication and distribution of resources available, and creates shared sample and data biobanks and recruiting database of mothers, infants, children, adolescents and adults with diabetes, diabetes risk and controls.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Clinical Resource Core Facility (RRID:SCR_022903) Copy
https://www.atypicaldiabetesnetwork.org/
Portal dedicated to characterizing, discovering and defining rare and atypical forms of diabetes. Network of universities, hospitals and clinics across the United States dedicated to better understanding atypical diabetes. Team of academic institutions and scientists collaborates with physicians and healthcare groups to identify those with atypical diabetes and learn more about their health.
Proper citation: Rare and Atypical Diabetes Network (RRID:SCR_024732) Copy
Web interactive browser to visualize data and perform gene set enrichment analysis along with gene and SNP lookup. Web interface used to query STARNET datasets and downstream analysis which includes RNAseq from 7 tissues: blood, free internal mammary artery (MAM), atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV). Paired SNP genotyping data is included and utilized for tissue expression quantitative trait loci (eQTL), CAD heritability (H2), co-expression networks and gene regulatory networks.
Proper citation: STARNET (RRID:SCR_025238) Copy
Core that provides services related to the application of genetic methodologies to research related to diabetes. Services include generation of targeted genetic mouse models, using CRISPR/Cas9 system in mouse or rat embryos, generation of specialty viral vectors, specialty viral reagents, and specialty mouse models.
Proper citation: Michigan Diabetes Research Center Molecular Genetics Core Facility (RRID:SCR_015119) Copy
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