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

DOI: 10.18129/B9.bioc.metagene    

This is the development version of metagene; for the stable release version, see metagene.

A package to produce metagene plots

Bioconductor version: Development (3.7)

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>, Cedric Lippens <lippens.cedric at protonmail>, 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
HTML R Script Introduction to metagene
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 2.11.1
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 3.4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr
LinkingTo
Suggests BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown
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.

Source Package metagene_2.11.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) metagene_2.11.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/metagene
Package Short Url http://bioconductor.org/packages/metagene/
Package Downloads Report Download Stats

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