To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

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>

Citation (from within R, enter citation("SplicingGraphs")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SplicingGraphs")

 

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

Details

biocViews Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Software, Visualization
Version 1.4.1
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(>= 1.0.3), 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
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source SplicingGraphs_1.4.1.tar.gz
Windows Binary SplicingGraphs_1.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SplicingGraphs_1.4.1.tgz
Mac OS X 10.9 (Mavericks) SplicingGraphs_1.4.1.tgz
Browse/checkout source (username/password: readonly)
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