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