prober-manuscript

Analysis code for the manuscript:

PROBER Identifies Proteins Associated with Sequence-Specific DNA in Living Cells
Mondal, et al. 2022.

Install conda environment

Use conda or mamba to avoid installing required packages independently.

mamba env create -f conda/env.yaml -n prober-analysis
conda activate prober-analysis

Download ENCODE data used in study

source analysis/0-download_encode_data.sh

Run analysis scripts

For example:

Rscript --vanilla analysis/1-PROBER-MS_contrasts.R

Inspect results

ls results/