Package: genomation
Type: Package
Title: Summary, annotation and visualization of genomic data
Version: 1.0.0
Author: Altuna Akalin, Vedran Franke
Maintainer: Altuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
Description: 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.
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
biocViews: Annotation, Sequencing, Visualization, CpGIsland
Encoding: latin1
Depends: R (>= 3.0.0),grid
Imports: GenomicRanges, GenomicAlignments, IRanges, Rsamtools,
        data.table, plyr, reshape2, ggplot2, methods, rtracklayer,
        gridBase, impute
Suggests: RUnit, knitr, RColorBrewer, genomationData, BiocGenerics,
        rmarkdown, knitrBootstrap
Collate: 'documentData.R' 'genomation-classes.R'
        'getRandomEnrichment.R' 'findFeatureComb.R' 'plotMatrix.R'
        'randomizeFeature.R' 'readAnnotate.R' 'readData.R'
        'scoreMatrix.R' 'scoreMatrixBin.R' 'scoreMatrixList.R'
        'test_genomation_package.R'
NeedsCompilation: no
Packaged: 2015-04-17 05:41:45 UTC; biocbuild
Built: R 3.2.0; ; 2015-04-17 09:06:47 UTC; windows
