COTAN
COexpression Tables ANalysis
Bioconductor version: Release (3.20)
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("COTAN")):
Installation
To install this package, start R (version "4.4") 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")| Guided tutorial to COTAN V.2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics |
| Version | 2.6.1 |
| 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 |
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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | COTAN_2.6.1.tar.gz |
| Windows Binary (x86_64) | COTAN_2.6.1.zip |
| macOS Binary (x86_64) | COTAN_2.6.0.tgz |
| macOS Binary (arm64) | COTAN_2.6.0.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 |
| Old Source Packages for BioC 3.20 | Source Archive |