COTAN

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

COexpression Tables ANalysis

Bioconductor version: Development (3.21)

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] (ORCID: ), Morandin Francesco [aut] (ORCID: ), Fantozzi Marco [aut] (ORCID: ), Pietrosanto Marco [aut] (ORCID: ), Puttini Daniel [aut] (ORCID: ), Priami Corrado [aut] (ORCID: ), Cremisi Federico [aut] (ORCID: ), Helmer-Citterich Manuela [aut] (ORCID: )

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics
Version	2.7.1
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL-3
Depends	R (>= 4.3)
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, SingleCellExperiment, SummarizedExperiment, S4Vectors
System Requirements
URL	https://github.com/seriph78/COTAN
Bug Reports	https://github.com/seriph78/COTAN/issues

Suggests	testthat (>= 3.2.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	COTAN_2.7.1.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	COTAN_2.7.1.tgz
macOS Binary (arm64)	COTAN_2.7.1.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