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    24 repositories

    • gene_lists

      Public
      List of gene lists for genomic analyses.
      Python
      •81•215•3•0•Updated Jun 24, 2022Jun 24, 2022

    • tx_annotation

      Public
      Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation"
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•33•3•0•Updated May 5, 2022May 5, 2022

    • gnomad_mnv

      Public
      Multi-nucleotide variants (MNVs) in gnomAD 2.1
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•11•2•0•Updated Feb 22, 2022Feb 22, 2022

    • gnomad_lrrk2

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Feb 22, 2022Feb 22, 2022

    • gnomad_browser

      Public archive
      gnomAD browser pre-ASHG 2018
      JavaScript
      •
      MIT License
      •16•33•0•0•Updated Nov 2, 2020Nov 2, 2020

    • clinvar

      Public
      This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
      Python
      •
      Other
      •55•122•6•2•Updated Feb 13, 2020Feb 13, 2020

    • MyoSeq_reports

      Public
      Creates research-only pdf reports for MyoSeq group
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 13, 2020Jan 13, 2020

    • cromwell_intro

      Public
      Dockerfile and wdl script for a simple cromwell / firecloud workflow
      WDL
      •
      MIT License
      •1•0•0•0•Updated Sep 3, 2019Sep 3, 2019

    • gnomad-docs

      Public
      0•0•0•0•Updated Jul 29, 2019Jul 29, 2019

    • igv_utils

      Public
      utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
      JavaScript
      •11•48•7•1•Updated May 7, 2019May 7, 2019

    • matchbox

      Public
      matchbox server for the Matchmaker Exchange
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•7•0•Updated Nov 26, 2018Nov 26, 2018

    • exac_browser

      Public archive
      Archive of ExAC browser
      JavaScript
      •
      MIT License
      •54•0•0•0•Updated Nov 2, 2018Nov 2, 2018

    • hail

      Public
      Scalable genetic data analysis.
      Scala
      •
      MIT License
      •246•0•0•0•Updated Oct 8, 2018Oct 8, 2018

    • elasticsearch-kubernetes-cluster

      Public archive
      Scripts for deploying a stand-alone elasticsearch cluster - based on https://github.com/pires/kubernetes-elasticsearch-cluster
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 11, 2017Sep 11, 2017

    • obo_parser

      Public
      Parses ontologies in .obo format (such as the Human Phenotype Ontology) and converts them to a .tsv table.
      Python
      •
      MIT License
      •8•5•1•1•Updated May 24, 2017May 24, 2017

    • exac-readviz

      Public
      Scripts used to generate the reassembled HaplotypeCaller -bamout bams that underly the read data visualizations which appear at the bottom of ExAC browser variant pages.
      Python
      •
      MIT License
      •1•2•1•0•Updated Apr 24, 2017Apr 24, 2017

    • exac_2015

      Public
      Companion repo for ExAC paper, 2015
      R
      •
      MIT License
      •13•33•5•0•Updated Oct 10, 2016Oct 10, 2016

    • omim

      Public
      Repo for downloading and storing OMIM data
      Python
      •9•18•1•1•Updated Oct 6, 2016Oct 6, 2016

    • Spidex

      Public
      VEP plugin which annotates variants with Spidex scores (see http://www.deepgenomics.com/spidex/)
      Python
      •1•3•2•0•Updated Jul 25, 2016Jul 25, 2016

    • ssDist

      Public
      VEP plugin which annotates variants with distance to nearest splice sites
      Perl
      •2•0•0•0•Updated Jul 25, 2016Jul 25, 2016

    • dbass

      Public
      Database of de novo and cryptic splice site variants
      Python
      •3•0•0•0•Updated Jul 25, 2016Jul 25, 2016

    • exon_skipping

      Public
      Collection of manually-curated variants that cause exon skipping
      E
      •2•3•0•0•Updated Jul 18, 2016Jul 18, 2016

    • ribosome_occupancy

      Public
      Python
      •0•0•0•0•Updated Jan 8, 2015Jan 8, 2015

    • leiden_sc

      Public
      Repository to practice code review and best development practices with Software Carpentry.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•1•1•Updated Mar 26, 2014Mar 26, 2014