To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("metagene")
In most cases, you don't need to download the package archive at all.
Bioconductor version: 3.2
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>, 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")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagene")
HTML | metagene: a package to produce metagene plots | |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
Version | 2.2.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (1.5 years) |
License | Artistic-2.0 | file LICENSE |
Depends | R (>= 3.2.0), R6 (>= 2.0), GenomicRanges, BiocParallel |
Imports | rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP |
LinkingTo | |
Suggests | RUnit, BiocGenerics, 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.
Package Source | metagene_2.2.1.tar.gz |
Windows Binary | metagene_2.2.1.zip |
Mac OS X 10.6 (Snow Leopard) | metagene_2.2.0.tgz |
Mac OS X 10.9 (Mavericks) | metagene_2.2.1.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/metagene/tree/release-3.2 |
Package Short Url | http://bioconductor.org/packages/metagene/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: