coseq

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see coseq.

Co-Expression Analysis of Sequencing Data


Bioconductor version: 3.6

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 jouy.inra.fr>

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

Installation

To install this package, start R (version "3.4") and enter:


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

BiocManager::install("coseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, RNASeq, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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Package Archives

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

Source Package coseq_1.2.0.tar.gz
Windows Binary coseq_1.2.0.zip
Mac OS X 10.11 (El Capitan) coseq_1.2.0.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/
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Old Source Packages for BioC 3.6 Source Archive