Package: SplicingGraphs
Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
	to them
Version: 1.5.2
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
License: Artistic-2.0
Description: This package allows the user to create, manipulate, and visualize
	splicing graphs and their bubbles based on a gene model for a given
	organism. Additionally it allows the user to assign RNA-seq reads to
	the edges of a set of splicing graphs, and to summarize them in
        different ways.
Maintainer: H. Pages <[email protected]>
Depends: BiocGenerics,
	 S4Vectors (>= 0.1.0), IRanges (>= 1.99.21), GenomicRanges (>= 1.17.22),
	 GenomicFeatures (>= 1.17.3), GenomicAlignments (>= 1.1.22),
	 Rgraphviz (>= 2.3.7)
Imports: methods, utils, igraph,
	 BiocGenerics,
	 IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
	 graph, Rgraphviz
Suggests: igraph, Gviz, Rsamtools,
	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,
	 RUnit
Collate: utils.R
	 igraph-utils.R
	 SplicingGraphs-class.R
	 plotTranscripts-methods.R
	 sgedgesByGene-methods.R
	 txpath-methods.R
	 sgedges-methods.R
	 sgraph-methods.R
	 rsgedgesByGene-methods.R
	 bubbles-methods.R
	 assignReads.R
	 countReads-methods.R
	 toy_data.R
	 zzz.R
biocViews: Genetics, Annotation, DataRepresentation, Visualization, Sequencing, RNASeq, GeneExpression