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COTAN

This is the development version of COTAN; for the stable release version, see COTAN.

COexpression Tables ANalysis


Bioconductor version: Development (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 di.unipi.it>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Guided tutorial to COTAN V.2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version 2.3.3
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
System Requirements
URL https://github.com/seriph78/COTAN
Bug Reports https://github.com/seriph78/COTAN/issues
See More
Suggests testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf
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Package Archives

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

Source Package COTAN_2.3.3.tar.gz
Windows Binary COTAN_2.3.3.zip (64-bit only)
macOS Binary (x86_64) COTAN_2.3.3.tgz
macOS Binary (arm64) COTAN_2.3.3.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