xinwrli

RNABERT-2

gene_lists

List of gene lists for genomic analyses.

gtex-v8

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

rpe

The RPE project

topmed_freeze3_calling

TOPMed Freeze 3 variant calling pipeline

2019_rare_disease_bloodRNAseq_paper

Pipeline and analyses performed in the blood RNA-seq paper

2015_eigenMT_paper

PyVCF

A Variant Call Format reader for Python.

DOQTL

QTL mapping for Diversity Outbred mice (and other multi-founder advanced intercrosses)

gtex

GTEx analysis scripts

blood_rnaseq_rare_disease_paper

wdl

Workflow Description Language - Specification and Implementations

gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

gvanno

Generic human DNA variant annotation pipeline

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

atac-seq-pipeline

ENCODE ATAC-seq pipeline

STAR

RNA-seq aligner

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

rna-seq-pipeline

ATAC-seq

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

loftee

dox

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

ultra_rare_pheno_spectrum

RIVER

R package for RIVER (RNA-Informed Variant Effect on Regulation)

GTExV6PRareVariation

Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript