metagene2

DOI: 10.18129/B9.bioc.metagene2    

A package to produce metagene plots

Bioconductor version: Release (3.10)

This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

Author: Eric Fournier [cre, aut], Charles Joly Beauparlant [aut], Cedric Lippens [aut], Arnaud Droit [aut]

Maintainer: Eric Fournier <fournier.eric.2 at crchudequebec.ulaval.ca>

Citation (from within R, enter citation("metagene2")):

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("metagene2")

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("metagene2")

 

HTML R Script Introduction to metagene2
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 1.2.1
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License Artistic-2.0
Depends R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, DBChIP, purrr, data.table, methods, dplyr, magrittr
LinkingTo
Suggests BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
SystemRequirements
Enhances
URL https://github.com/ArnaudDroitLab/metagene2
BugReports https://github.com/ArnaudDroitLab/metagene2/issues
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 metagene2_1.2.1.tar.gz
Windows Binary metagene2_1.2.1.zip
Mac OS X 10.11 (El Capitan) metagene2_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/metagene2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metagene2
Package Short Url https://bioconductor.org/packages/metagene2/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive

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