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https://github.com/broadinstitute/gtex-v8

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

https://github.com/broadinstitute/gtex-v8

Science Score: 36.0%

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    Links to: ncbi.nlm.nih.gov
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Last synced: 10 months ago · JSON representation

Repository

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 122 MB
Statistics
  • Stars: 41
  • Watchers: 4
  • Forks: 13
  • Open Issues: 2
  • Releases: 1
Created almost 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

GTEx V8

This repository contains notebooks and scripts for reproducing analyses and figures from the paper The GTEx Consortium atlas of genetic regulatory effects across human tissues, Science, 2020.

Requirements

The following Python modules are needed to run the notebooks: numpy, pandas, scipy, ipython, jupyter, matplotlib, seaborn, qtl

The notebooks require data from the GTEx Portal to run (by default, the data is assumed to be accessible in the data directory of this repository). Running the following commands will download the relevant files: ``` cd data

QTLs

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8eQTL.tar && \ tar xf GTExAnalysisv8eQTL.tar && rm GTExAnalysisv8eQTL.tar

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8sQTL.tar && \ tar xf GTExAnalysisv8sQTL.tar && rm GTExAnalysisv8sQTL.tar

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8eQTLindependent.tar && \ tar xf GTExAnalysisv8eQTLindependent.tar && rm GTExAnalysisv8eQTL_independent.tar

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8sQTLindependent.tar && \ tar xf GTExAnalysisv8sQTLindependent.tar && rm GTExAnalysisv8sQTL_independent.tar

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8transeGenesfdr05.txt

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8transsGenesfdr05.txt

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8eQTLexpressionmatrices.tar && \ tar xf GTExAnalysisv8eQTLexpressionmatrices.tar && rm GTExAnalysisv8eQTLexpressionmatrices.tar

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8eQTLcovariates.tar.gz && \ tar xf GTExAnalysisv8eQTLcovariates.tar.gz && rm GTExAnalysisv8eQTL_covariates.tar.gz

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExAnalysisv8sQTLgroups.tar.gz && \ tar xf GTExAnalysisv8sQTLgroups.tar.gz && rm GTExAnalysisv8sQTL_groups.tar.gz

fine mapping results

wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExv8finemappingCAVIAR.tar && \ tar xf GTExv8finemappingCAVIAR.tar && rm GTExv8finemappingCAVIAR.tar wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExv8finemappingCaVEMaN.tar && \ tar xf GTExv8finemappingCaVEMaN.tar && rm GTExv8finemappingCaVEMaN.tar wget https://storage.googleapis.com/gtexanalysisv8/singletissueqtldata/GTExv8finemappingDAPG.tar && \ tar xf GTExv8finemappingDAPG.tar && rm GTExv8finemappingDAPG.tar

annotation

wget https://storage.googleapis.com/gtexanalysisv8/reference/gencode.v26.GRCh38.genes.gtf wget https://storage.googleapis.com/gtexanalysisv8/reference/WGSFeatureoverlapcollapsedVEPshort4torus.MAF01.txt.gz ```

A subset of the figures require genotype information. The VCF can be obtained from dbGaP (accession phs000424) or from AnVIL (requires dbGaP authentication).

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

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