This repository contains code and data for generating figures to Jeong and Bulyk (in prep).
Updated April 16th 2023. Raehoon Jeong (rjeong@g.harvard.edu), Martha Bulyk Lab (mlbulyk@genetics.med.harvard.edu).
- Genome track images of PU.1 ChIP-seq, ATAC-seq, etc. were generated using IGV browser.
- Fuji plot in Figure 3 was generated using code from Masahiro Kanai.
- Canonical transcripts of genes were plotted using database from Locusviz.
- The legend for colors reflecting LD with selected variants were added manually.
- Relevant analyses scripts are included in PU1-colocalization-manuscript/code/analysis directory.
- For the other R scripts, the following packages need to be installed.
ggplot2
dplyr
cowplot
forcats
patchwork
data.table
AnnotationDbi
Ggbio
GenomicRanges
locuscomparer
ComplexUpset
- Clone the repository
git clone git@github.com:BulykLab/PU1-colocalization-manuscript.git
- Move to the code directory
cd PU1-colocalization-manuscript/code
- Run each code to generate figures using R
Rscript Figure2.R # or any other code in the directory