Single cell local gene co-expression pairs (COP) project

This repository contains scripts for data processing, analysis and figure generation data for our preprint:

Ribeiro DM, Ziyani C, Delaneau O. Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis. Communications Biology (2022).

Analysis scripts

• CODer.py : Script to identify local co-expressed gene pairs (COPs) given a gene expression matrix. Example usage: python3 CODer.py expression_matrix.bed output_folder 1000 --fdrCutoff 0.01 --lowMem 1
• ShareSeqCoex.py Script to identify co-expressed gene-peak pairs from single cell a atac-seq and gene expression in same cells. Example usage: python3 ShareSeqCoex.py gene_matrix.tsv peak_matrix.tsv gencode_v19.bed output_file.txt
• cuomo / share_seq / sarkar : Folder with all scripts used to produce figures for the paper, split by dataset

Data availability

Data on co-expressed genes discovered here are available for consultation and download through the LoCOP DB database.

License

LoCOP is available under a MIT license. For more information please see the LICENSE.