macarthur-lab/leiden_sc

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macarthur-lab/leiden_sc

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Repository to practice code review and best development practices with Software Carpentry.

gene_lists

List of gene lists for genomic analyses.

clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

igv_utils

utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.

gnomad_browser

gnomAD browser pre-ASHG 2018

tx_annotation

Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation"

exac_2015

Companion repo for ExAC paper, 2015

omim

Repo for downloading and storing OMIM data

gnomad_mnv

Multi-nucleotide variants (MNVs) in gnomAD 2.1

Jupyter Notebook

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.

gnomad_lrrk2

Spidex

VEP plugin which annotates variants with Spidex scores (see http://www.deepgenomics.com/spidex/)

exon_skipping

Collection of manually-curated variants that cause exon skipping

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.

elasticsearch-kubernetes-cluster

Scripts for deploying a stand-alone elasticsearch cluster - based on https://github.com/pires/kubernetes-elasticsearch-cluster