coseq

DOI: 10.18129/B9.bioc.coseq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see coseq.

Co-Expression Analysis of Sequencing Data

Bioconductor version: 3.9

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, Cathy Maugis-Rabusseau, Antoine Godichon-Baggioni

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	coseq
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL (>=3)
Depends	R (>= 3.4.0), SummarizedExperiment, S4Vectors
Imports	edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2 (>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8), grDevices, graphics, stats, methods, compositions, mvtnorm
LinkingTo
Suggests	Biobase, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	coseq_1.8.0.tar.gz
Windows Binary	coseq_1.8.0.zip
Mac OS X 10.11 (El Capitan)	coseq_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/coseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/coseq
Package Short Url	https://bioconductor.org/packages/coseq/
Package Downloads Report	Download Stats