COTAN
This is thereleased version of COTAN; for the devel version, seeCOTAN.
COexpression Tables ANalysis
Bioconductor version: Release (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("COTAN")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("COTAN")For older versions of R, please refer to the appropriateBioconductor 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 | 2.10.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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 |
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| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | COTAN_2.10.0.tar.gz |
| Windows Binary (x86_64) | COTAN_2.10.0.zip |
| macOS Binary (x86_64) | COTAN_2.10.0.tgz |
| macOS Binary (arm64) | COTAN_2.10.0.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 |