To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genomation")

In most cases, you don't need to download the package archive at all.

genomation

 

   

This is the development version of genomation; for the stable release version, see genomation.

Summary, annotation and visualization of genomic data

Bioconductor version: Development (3.4)

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Liz Ing-Simmons [ctb]

Maintainer: Altuna Akalin <aakalin at gmail.com>, Vedran Franke <vedran.franke at gmail.com>

Citation (from within R, enter citation("genomation")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genomation")

Documentation

HTML R Script genomation
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, CpGIsland, Sequencing, Software, Visualization
Version 1.5.2
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License Artistic-2.0
Depends R (>= 3.0.0), grid
Imports Biostrings, BSgenome, data.table, GenomeInfoDb, GenomicRanges(>= 1.23.26), GenomicAlignments, S4Vectors(>= 0.9.25), ggplot2, gridBase, impute, IRanges, matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools, seqPattern, rtracklayer
LinkingTo
Suggests BiocGenerics, genomationData, knitr, knitrBootstrap, RColorBrewer, rmarkdown, RUnit
SystemRequirements
Enhances
URL http://bioinformatics.mdc-berlin.de/genomation/
BugReports https://github.com/BIMSBbioinfo/genomation/issues
Depends On Me
Imports Me CexoR
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source genomation_1.5.2.tar.gz
Windows Binary genomation_1.5.2.zip
Mac OS X 10.9 (Mavericks) genomation_1.5.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/genomation
Package Short Url http://bioconductor.org/packages/genomation/
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