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metagene2

A package to produce metagene plots


Bioconductor version: Release (3.18)

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 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL https://github.com/ArnaudDroitLab/metagene2
Bug Reports https://github.com/ArnaudDroitLab/metagene2/issues
See More
Suggests BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
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Package Archives

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

Source Package metagene2_1.18.0.tar.gz
Windows Binary metagene2_1.18.0.zip
macOS Binary (x86_64) metagene2_1.18.0.tgz
macOS Binary (arm64) metagene2_1.18.0.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