DOI: 10.18129/B9.bioc.COTAN    

COexpression Tables ANalysis

Bioconductor version: Release (3.15)

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] , Pietrosanto Marco [aut] , Cremisi Federico [aut] , Helmer-Citterich Manuela [aut]

Maintainer: Galfrè Silvia Giulia <silvia.galfre at>

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biocViews GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.1)
Imports dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, stats, parallel, tibble, tidyr, basilisk, reticulate, ComplexHeatmap, circlize, grid, scales, utils, rlang, Rfast
Suggests testthat (>= 3.0.0), spelling, knitr, data.table, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, factoextra, Rtsne, plotly, dendextend, BiocStyle, cowplot
SystemRequirements python
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