Package: SplicingGraphs
Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
	to them
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.
biocViews: Genetics, Annotation, DataRepresentation, Visualization,
	Sequencing, RNASeq, GeneExpression, AlternativeSplicing, Transcription,
	ImmunoOncology
URL: https://bioconductor.org/packages/SplicingGraphs
BugReports: https://github.com/Bioconductor/SplicingGraphs/issues
Version: 1.51.1
License: Artistic-2.0
Encoding: UTF-8
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès
Maintainer: H. Pagès <hpages.on.github@gmail.com>
Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
	 Rgraphviz (>= 2.3.7)
Imports: methods, utils, graphics, igraph, BiocGenerics,
	 S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2),
	 Seqinfo, GenomicRanges (>= 1.23.21), Rsamtools, graph
Suggests: igraph, Gviz, txdbmaker,
	 TxDb.Hsapiens.UCSC.hg19.refGene, 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
git_url: https://git.bioconductor.org/packages/SplicingGraphs
git_branch: devel
git_last_commit: 8abbef9
git_last_commit_date: 2025-11-02
Repository: Bioconductor 3.23
