Bioconductor version: Release (3.6)
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")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("metagene")
HTML | R Script | Introduction to metagene |
HTML | R Script | Introduction to metagene |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
Version | 2.10.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (3.5 years) |
License | Artistic-2.0 | file LICENSE |
Depends | R (>= 3.4.0), 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 |
LinkingTo | |
Suggests | RUnit, BiocGenerics, similaRpeak, knitr, BiocStyle, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
BugReports | https://github.com/CharlesJB/metagene/issues |
Depends On Me | Imetagene |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | metagene_2.10.1.tar.gz |
Windows Binary | metagene_2.10.1.zip |
Mac OS X 10.11 (El Capitan) | metagene_2.10.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/metagene |
Package Short Url | http://bioconductor.org/packages/metagene/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.6 | Source Archive |
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