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>
citation("coseq")):
Installation
To install this package, start R (version "3.6") 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
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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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 |
| System Requirements | |
| URL |
See More
| Suggests | Biobase, knitr, rmarkdown, testthat |
| 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_1.10.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/coseq/ |
| Package Short Url | https://bioconductor.org/packages/coseq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |