Pinned Repositories
clinvar
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
exac_2015
Companion repo for ExAC paper, 2015
gene_lists
List of gene lists for genomic analyses.
gnomad_browser
gnomAD browser pre-ASHG 2018
gnomad_mnv
Multi-nucleotide variants (MNVs) in gnomAD 2.1
igv_utils
utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
matchbox
matchbox server for the Matchmaker Exchange
obo_parser
Parses ontologies in .obo format (such as the Human Phenotype Ontology) and converts them to a .tsv table.
omim
Repo for downloading and storing OMIM data
tx_annotation
Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation"
MacArthur Lab's Repositories
macarthur-lab/gene_lists
List of gene lists for genomic analyses.
macarthur-lab/clinvar
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
macarthur-lab/igv_utils
utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
macarthur-lab/exac_2015
Companion repo for ExAC paper, 2015
macarthur-lab/gnomad_browser
gnomAD browser pre-ASHG 2018
macarthur-lab/tx_annotation
Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation"
macarthur-lab/omim
Repo for downloading and storing OMIM data
macarthur-lab/gnomad_mnv
Multi-nucleotide variants (MNVs) in gnomAD 2.1
macarthur-lab/matchbox
matchbox server for the Matchmaker Exchange
macarthur-lab/obo_parser
Parses ontologies in .obo format (such as the Human Phenotype Ontology) and converts them to a .tsv table.
macarthur-lab/exon_skipping
Collection of manually-curated variants that cause exon skipping
macarthur-lab/gnomad_lrrk2
macarthur-lab/leiden_sc
Repository to practice code review and best development practices with Software Carpentry.
macarthur-lab/Spidex
VEP plugin which annotates variants with Spidex scores (see http://www.deepgenomics.com/spidex/)
macarthur-lab/exac-readviz
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.
macarthur-lab/elasticsearch-kubernetes-cluster
Scripts for deploying a stand-alone elasticsearch cluster - based on https://github.com/pires/kubernetes-elasticsearch-cluster
macarthur-lab/gnomad-docs
macarthur-lab/cromwell_intro
Dockerfile and wdl script for a simple cromwell / firecloud workflow
macarthur-lab/dbass
Database of de novo and cryptic splice site variants
macarthur-lab/exac_browser
Archive of ExAC browser
macarthur-lab/hail
Scalable genetic data analysis.
macarthur-lab/MyoSeq_reports
Creates research-only pdf reports for MyoSeq group
macarthur-lab/ribosome_occupancy
macarthur-lab/ssDist
VEP plugin which annotates variants with distance to nearest splice sites