coseq

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

Co-Expression Analysis of Sequencing Data

Bioconductor version: Development (3.21)

Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

Author: Andrea Rau [cre, aut] (ORCID: ), Cathy Maugis-Rabusseau [ctb], Antoine Godichon-Baggioni [ctb]

Maintainer: Andrea Rau <andrea.rau at inrae.fr>

Citation (from within R, enter citation("coseq")):

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("coseq")

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("coseq")

coseq	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.31.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 years)
License	GPL-3
Depends	R (>= 4.0.0), SummarizedExperiment, S4Vectors
Imports	edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm
System Requirements
URL

Suggests	Biobase, knitr, rmarkdown, testthat, BiocStyle
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	coseq_1.31.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/coseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/coseq
Bioc Package Browser	https://code.bioconductor.org/browse/coseq/
Package Short Url	https://bioconductor.org/packages/coseq/
Package Downloads Report	Download Stats