metagene
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see metagene.
A package to produce metagene plots
Bioconductor version: 3.9
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("metagene")
):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")
Introduction to metagene | HTML | R Script |
RNA-seq exp ext | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
Version | 2.16.0 |
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, muStat, Rsamtools, DBChIP, 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, similaRpeak |
Linking To | |
Enhances | |
Depends On Me | Imetagene |
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_2.16.0.tar.gz |
Windows Binary | metagene_2.16.0.zip |
Mac OS X 10.11 (El Capitan) | metagene_2.16.0.tgz |
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 |
Old Source Packages for BioC 3.9 | Source Archive |