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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.
metagene
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A package to produce metagene plots
Bioconductor version: Release (3.4)
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("metagene")
Documentation
| HTML | R Script | Introduction to metagene |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Alignment, ChIPSeq, Coverage, Genetics, MultipleComparison, Sequencing, Software |
| Version | 2.6.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 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, matrixStats |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown, similaRpeak |
| SystemRequirements | |
| Enhances | |
| URL | |
| BugReports | https://github.com/CharlesJB/metagene/issues |
| Depends On Me | Imetagene |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | metagene_2.6.1.tar.gz |
| Windows Binary | metagene_2.6.1.zip |
| Mac OS X 10.9 (Mavericks) | metagene_2.6.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/metagene/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/metagene/ |
| Package Downloads Report | Download Stats |
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