coseq

DOI: 10.18129/B9.bioc.coseq    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see coseq.

Co-Expression Analysis of Sequencing Data

Bioconductor version: 3.10

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	1.10.0
In Bioconductor since	BioC 3.5 (R-3.4) (3 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
Links To Me
Build Report

Package Archives

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

Source Package	coseq_1.10.0.tar.gz
Windows Binary	coseq_1.10.0.zip
Mac OS X 10.11 (El Capitan)	coseq_1.10.0.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