COTAN
This is the released version of COTAN; for the devel version, see COTAN.
COexpression Tables ANalysis
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Cleaning tutorial using COTAN | HTML | R Script |
| DEA using COTAN | HTML | R Script |
| Genes' clustering using COTAN | HTML | R Script |
| Uniform clustering using COTAN | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DifferentialExpression, GPU, GeneExpression, SingleCell, Software, SystemsBiology, Transcriptomics |
| Version | 2.12.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.3) |
| Imports | stats, methods, grDevices, Matrix, ggplot2, ggrepel, ggdist, ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr, BiocSingular, parallelDist, ComplexHeatmap, BiocStyle, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, dendextend, zeallot, conflicted, assertthat, R.utils, withr, SummarizedExperiment, SingleCellExperiment, proxy, RSpectra, GEOquery |
| 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, ragg, Cairo, data.table, gsubfn, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, cowplot, qpdf, sf, torch, 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.
| Source Package | COTAN_2.12.1.tar.gz |
| Windows Binary (x86_64) | COTAN_2.12.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | COTAN_2.12.1.tgz |
| macOS Binary (sonoma-arm64) | COTAN_2.12.1.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 |
| Old Source Packages for BioC 3.23 | Source Archive |