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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("metagene")
In most cases, you don't need to download the package archive at all.
metagene
A package to produce metagene plots
Bioconductor version: 3.0
This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Pre-calculated features (such as transcription start sites of protein coding gene or enhancer) are available. Bam files are used to increase the resolution. Multiple combination of group of features and or group of bam files 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:
source("http://bioconductor.org/biocLite.R")
biocLite("metagene")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagene")
| HTML | R Script | A package to produce Metafeature plots |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, Genetics, MultipleComparison, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | rtracklayer, GenomicRanges, GenomicAlignments, ggplot2 |
| Imports | |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, knitr |
| SystemRequirements | |
| Enhances | parallel, biomaRt |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | metagene_1.0.0.tar.gz |
| Windows Binary | metagene_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | metagene_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | metagene_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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