COTAN

DOI: 10.18129/B9.bioc.COTAN    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see COTAN.

COexpression Tables ANalysis

Bioconductor version: 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 uniroma1.it>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("COTAN")

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

Documentation

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

browseVignettes("COTAN")

 

HTML	R Script	Guided tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
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
LinkingTo
Suggests	testthat (>= 3.0.0), spelling, knitr, data.table, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, factoextra, Rtsne, plotly, dendextend, BiocStyle, cowplot
SystemRequirements	python
Enhances
URL	https://github.com/seriph78/COTAN
BugReports	https://github.com/seriph78/COTAN/issues
Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	COTAN_1.0.0.tar.gz
Windows Binary	COTAN_1.0.0.zip
macOS Binary (x86_64)	COTAN_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/COTAN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/COTAN
Package Short Url	https://bioconductor.org/packages/COTAN/
Package Downloads Report	Download Stats