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@T2DREAM Common Metabolic Disease Genome Atlas

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    24 repositories

    • t2dream-portal

      Public
      The Common Metabolic Disease Genome Atlas (CMDGA) resource is a component of AMP-CMD being developed at the University of California San Diego as part of a larger consortium of academic, industry and non-profit institutions worldwide. The resource is based on software developed by the ENCODE DCC at Stanford University.
      Python
      •
      MIT License
      •8•4•0•3•Updated Jul 25, 2024Jul 25, 2024

    • snovault

      Public
      The resource is based on software developed by the ENCODE DCC at Stanford University.
      Python
      •
      MIT License
      •2•0•0•1•Updated May 23, 2023May 23, 2023

    • cellxgene-gateway

      Public
      Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
      Python
      •
      Apache License 2.0
      •32•0•0•0•Updated Jan 21, 2023Jan 21, 2023

    • variant-nw

      Public
      Variant Network Visualization Tool. Credit for Dash tool @smorabit
      Python
      •0•0•0•8•Updated Dec 26, 2022Dec 26, 2022

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated May 17, 2022May 17, 2022

    • demultiplex

      Public
      Pipeline for demultiplexing and doublet detection + checking method robustness
      1•0•0•0•Updated Dec 23, 2021Dec 23, 2021

    • dig-bioindex

      Public
      BIO index for genetic records stored in S3 and FastAPI server.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Nov 18, 2021Nov 18, 2021

    • dig-loam-stream

      Public
      dig-loam-stream
      Scala
      •
      Other
      •1•0•0•0•Updated Nov 18, 2021Nov 18, 2021

    • expression-profiling-app

      Public
      The Gene Expression Profiling App displays the snRNA-seq data
      R
      •
      MIT License
      •1•0•0•0•Updated Sep 7, 2021Sep 7, 2021

    • react-annotation-graph

      Public
      This application links Co-accessibility of distal regulatory variants to putative target genes
      JavaScript
      •0•1•0•2•Updated Jul 20, 2021Jul 20, 2021

    • lung-epigenome

      Public
      The goal of this project is to provide data on the genome and epigenome of the human lung to facilitate research efforts of investigators studying diseases of the lung including COVID-19.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 15, 2021Jul 15, 2021

    • crocpot

      Public
      CROCPOT is a repository of epigenomic datasets linking distal cis-regulatory elements to their putative target genes including 3D chromatin interactions, single cell co-activity, activity-by-contact (ABC) and CRISPRi regulatory screens.
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated May 27, 2021May 27, 2021

    • cellxgene

      Public
      An interactive explorer for single-cell transcriptomics data
      JavaScript
      •
      MIT License
      •116•0•0•0•Updated Jan 5, 2021Jan 5, 2021

    • DGA-ubuntu-installation

      Public
      0•0•0•0•Updated Jun 16, 2020Jun 16, 2020

    • pyencoded-tools

      Public
      Scripts to add and release datasets (based on https://github.com/ENCODE-DCC/pyencoded-tools)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2020Feb 10, 2020

    • aws-genomics-workflows

      Public
      T2D AMP Consortium Genomics Workflows on AWS
      Shell
      •
      MIT No Attribution
      •0•0•0•1•Updated Jan 21, 2020Jan 21, 2020

    • igv-react

      Public
      JavaScript
      •1•0•0•0•Updated Aug 26, 2019Aug 26, 2019

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
      Nextflow
      •
      MIT License
      •699•0•0•0•Updated Jul 17, 2019Jul 17, 2019

    • igv.js

      Public
      Embeddable genomic visualization component based on the Integrative Genomics Viewer
      JavaScript
      •
      MIT License
      •227•0•0•0•Updated Jun 19, 2019Jun 19, 2019

    • igv-webapp

      Public
      IGV Web App
      JavaScript
      •
      MIT License
      •43•0•0•0•Updated Jun 19, 2019Jun 19, 2019

    • aws-cloudformation-templates

      Public
      A collection of useful CloudFormation templates
      Python
      •
      Apache License 2.0
      •4.3k•0•0•0•Updated Jun 11, 2019Jun 11, 2019

    • atacseq

      Public
      ATAC-seq peak-calling, QC and differential analysis pipeline.
      Nextflow
      •
      MIT License
      •116•0•0•0•Updated Jun 5, 2019Jun 5, 2019

    • rest-api

      Public
      T2DREAM application programming interface provides developers with a programmatic interface to query and download data
      Python
      •1•0•0•0•Updated Jun 14, 2018Jun 14, 2018

    • kentUtils

      Public
      UCSC command line bioinformatic utilities
      C
      •95•0•0•0•Updated Jun 8, 2017Jun 8, 2017