metagene2

A package to produce metagene plots

Bioconductor version: Release (3.17)

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 <ericfournier2 at yahoo.ca>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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")

Introduction to metagene2	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports	rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2
Linking To
Suggests	BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
System Requirements
Enhances
URL	https://github.com/ArnaudDroitLab/metagene2
Bug Reports	https://github.com/ArnaudDroitLab/metagene2/issues

Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	metagene2_1.16.0.tar.gz
Windows Binary	metagene2_1.16.0.zip
macOS Binary (x86_64)	metagene2_1.16.0.tgz
macOS Binary (arm64)	metagene2_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metagene2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metagene2
Bioc Package Browser	https://code.bioconductor.org/browse/metagene2/
Package Short Url	https://bioconductor.org/packages/metagene2/
Package Downloads Report	Download Stats