seriph78/COTAN: COexpression Tables ANalysis

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

Getting started

Package details

Bioconductor views GeneExpression SingleCell SystemsBiology Transcriptomics
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
seriph78/COTAN documentation built on July 2, 2024, 9:27 a.m.