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COexpression Tables ANalysis

Bioconductor version: Release (3.19)

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.

Author: Galfrè Silvia Giulia [aut, cre] , Morandin Francesco [aut] , Fantozzi Marco [aut] , Pietrosanto Marco [aut] , Puttini Daniel [aut] , Priami Corrado [aut] , Cremisi Federico [aut] , Helmer-Citterich Manuela [aut]

Maintainer: Galfrè Silvia Giulia <silvia.galfre at>

Citation (from within R, enter citation("COTAN")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Guided tutorial to COTAN V.2 HTML R Script
Reference Manual PDF


biocViews GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version 2.4.4
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2)
Imports stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, dendextend, zeallot, assertthat, withr
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Source Package COTAN_2.4.4.tar.gz
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macOS Binary (x86_64) COTAN_2.4.4.tgz
macOS Binary (arm64) COTAN_2.4.4.tgz
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