coseq

DOI: 10.18129/B9.bioc.coseq    

Co-Expression Analysis of Sequencing Data

Bioconductor version: Release (3.7)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("coseq")

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, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
License GPL (>=3)
Depends R (>= 3.4.1), SummarizedExperiment, S4Vectors
Imports edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2 (>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8), gridExtra, 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_1.4.0.tar.gz
Windows Binary coseq_1.4.0.zip
Mac OS X 10.11 (El Capitan) coseq_1.4.0.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 http://bioconductor.org/packages/coseq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: