metagene

DOI: 10.18129/B9.bioc.metagene    

A package to produce metagene plots

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("metagene")

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("metagene")

 

HTML	R Script	Introduction to metagene
HTML	R Script	RNA-seq exp ext
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version	2.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (7 years)
License	Artistic-2.0 | file LICENSE
Depends	R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
Imports	rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr
LinkingTo
Suggests	BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown, similaRpeak
SystemRequirements
Enhances
URL
BugReports	https://github.com/CharlesJB/metagene/issues
Depends On Me	Imetagene
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	metagene_2.24.0.tar.gz
Windows Binary	metagene_2.24.0.zip
macOS 10.13 (High Sierra)	metagene_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metagene
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metagene
Package Short Url	https://bioconductor.org/packages/metagene/
Package Downloads Report	Download Stats