To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

metagene

 

A package to produce metagene plots

Bioconductor version: Release (3.5)

This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.

Author: Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>, Fabien Claude Lamaze <fabien.lamaze.1 at ulaval.ca>, Rawane Samb <rawane.samb.1 at ulaval.ca>, Astrid Louise Deschenes <Astrid-Louise.Deschenes at crchudequebec.ulaval.ca> and Arnaud Droit <arnaud.droit at crchuq.ulaval.ca>.

Maintainer: Charles Joly Beauparlant <charles.joly-beauparlant at crchul.ulaval.ca>

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

Installation

To install this package, start R and enter:

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

Documentation

HTML R Script Introduction to metagene
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 2.8.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 3.2.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP, matrixStats
LinkingTo
Suggests RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown, similaRpeak
SystemRequirements
Enhances
URL
BugReports https://github.com/CharlesJB/metagene/issues
Depends On Me Imetagene
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source metagene_2.8.0.tar.gz
Windows Binary metagene_2.8.0.zip
Mac OS X 10.11 (El Capitan) metagene_2.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/metagene/tree/release-3.5
Package Short Url http://bioconductor.org/packages/metagene/
Package Downloads Report Download Stats

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