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metagene

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

A package to produce metagene plots


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software
Version 2.35.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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, Rsamtools, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr
System Requirements
URL
Bug Reports https://github.com/CharlesJB/metagene/issues
See More
Suggests BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package metagene_2.35.0.tar.gz
Windows Binary metagene_2.35.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/metagene
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metagene
Bioc Package Browser https://code.bioconductor.org/browse/metagene/
Package Short Url https://bioconductor.org/packages/metagene/
Package Downloads Report Download Stats