COTAN

DOI: 10.18129/B9.bioc.COTAN  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see COTAN.

COexpression Tables ANalysis

Bioconductor version: 3.17

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 di.unipi.it>

Installation

To install this package, start R (version "4.3") 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 as V.1
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version	2.0.5
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.2)
Imports	stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, irlba, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, factoextra, dendextend, zeallot, assertthat, withr
LinkingTo
Suggests	testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery
SystemRequirements
Enhances
URL	https://github.com/seriph78/COTAN
BugReports	https://github.com/seriph78/COTAN/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	COTAN_2.0.5.tar.gz
Windows Binary	COTAN_2.0.5.zip (64-bit only)
macOS Binary (x86_64)	COTAN_2.0.5.tgz
macOS Binary (arm64)	COTAN_2.0.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/COTAN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/COTAN
Bioc Package Browser	https://code.bioconductor.org/browse/COTAN/
Package Short Url	https://bioconductor.org/packages/COTAN/
Package Downloads Report	Download Stats