kauralasoo/macrophage-gxe-study

Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response

About

This repository contains the code used to analyse RNA-seq and ATAC-seq data from stimulated human macrophages, as described in this manuscript:

Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response https://www.biorxiv.org/content/early/2017/05/18/102392

Directories

• ATAC - scripts to analyise ATAC-seq data
• SL1344 - scripts to analysis RNA-seq data
• ATAC_RNA - scripts for joint analysis of RNA and ATAC-seq data
• Fairfax - scripts to analysis data from the Fairfax et al study
• covariates - construct sample metadata
• data - various small data files
• housekeeping - R package with project specifc functions
• munge - process genomic annotations
• public_chromatin - scripts to analyse processed public ChIP-seq datasets
• chromatin-scripts - Process raw ChIP-seq and ATAC-seq data

Dependencies

Many functions are imported from the seqUtils package: https://github.com/kauralasoo/seqUtils

macrophage-gxe-study's Issues

Script of rasqualToEigenMT

Hi Kaur,

I am trying to use EigenMT to eQTL mapped by rasqual.
I am wondering where can I find the code (rasqualToEigenMT.py) converting rasqual output to EigenMT input?

Thank you,
Hongbo

can get the related data?

Hello, very nice script. I want to test R Data analysis skills by learning your script, but I can't find related data. Would you mind providing the data or .rds? thxs!