PU1-colocalization-manuscript

This repository contains code and data for generating figures to Jeong and Bulyk (in prep).

Updated April 16th 2023. Raehoon Jeong ([email protected]), Martha Bulyk Lab ([email protected]).

Note

• 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

Workflow

1. Clone the repository

git clone [email protected]:BulykLab/PU1-colocalization-manuscript.git

2. Move to the code directory

cd PU1-colocalization-manuscript/code

3. Run each code to generate figures using R

Rscript Figure2.R   # or any other code in the directory