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Bioconductor - COTAN (development version)

COTAN

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

COexpression Tables ANalysis

Bioconductor version: Development (3.22)

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: 0000-0002-2770-0344 , Morandin Francesco [aut] ORCID: 0000-0002-2022-2300 , Fantozzi Marco [aut] ORCID: 0000-0002-0708-5495 , Pietrosanto Marco [aut] ORCID: 0000-0001-5129-6065 , Puttini Daniel [aut] ORCID: 0009-0006-8401-9949 , Priami Corrado [aut] ORCID: 0000-0002-3261-6235 , Cremisi Federico [aut] ORCID: 0000-0003-4925-2703 , Helmer-Citterich Manuela [aut] ORCID: 0000-0001-9530-7504

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")
Details biocViews GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics Version 2.9.4 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3 Depends R (>= 4.3) Imports stats, methods, grDevices, Matrix, ggplot2, ggrepel, gghalves, ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr, BiocSingular, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, dendextend, zeallot, assertthat, withr, SingleCellExperiment, proxy, RSpectra System Requirements URL https://github.com/seriph78/COTAN Bug Reports https://github.com/seriph78/COTAN/issues See More 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, SummarizedExperiment, S4Vectors 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.

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