SplicingGraphs

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:

    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	1.0.4
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
URL
Depends On Me
Imports Me
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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
Package Downloads Report	Download Stats

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