Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Bioconductor version: Release (2.12)

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.

Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages

Maintainer: H. Pages <hpages at fhcrc.org>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script Splicing graphs and RNA-seq data
PDF   Reference Manual


biocViews Annotation, DataRepresentation, GeneExpression, Genetics, RNAseq, Sequencing, Software, Visualization
Version 1.0.4
In Bioconductor since BioC 2.13 (R-2.18)
License Artistic-2.0
Depends BiocGenerics, IRanges(>= 1.17.43), GenomicRanges(>= 1.11.45), GenomicFeatures, Rgraphviz(>= 2.3.7)
Imports methods, utils, igraph, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures, graph, Rgraphviz
Suggests igraph, Gviz, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source SplicingGraphs_1.0.4.tar.gz
Windows Binary SplicingGraphs_1.0.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SplicingGraphs_1.0.4.tgz
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