SplicingGraphs

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

Bioconductor version: Release (2.14)

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:

    source("http://bioconductor.org/biocLite.R")
    biocLite("SplicingGraphs")

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

    citation("SplicingGraphs")

Documentation

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

Details

biocViews Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 2.12 (R-3.0)
License Artistic-2.0
Depends BiocGenerics, IRanges(>= 1.17.43), GenomicRanges(>= 1.15.12), GenomicFeatures, GenomicAlignments(>= 0.99.6), 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
System Requirements
URL
Depends On Me
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Package Downloads

Package Source SplicingGraphs_1.4.0.tar.gz
Windows Binary SplicingGraphs_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SplicingGraphs_1.4.0.tgz
Mac OS X 10.9 (Mavericks)
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