To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SplicingGraphs")

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

SplicingGraphs

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see SplicingGraphs.

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

Bioconductor version: 3.2

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 fredhutch.org>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 Splicing graphs and RNA-seq data
PDF Reference Manual

Details

biocViews AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.10.0
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License Artistic-2.0
Depends GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7)
Imports methods, utils, igraph, BiocGenerics, S4Vectors, IRanges(>= 2.3.21), GenomeInfoDb, GenomicRanges, GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz
LinkingTo
Suggests igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source SplicingGraphs_1.10.0.tar.gz
Windows Binary SplicingGraphs_1.10.0.zip
Mac OS X 10.6 (Snow Leopard) SplicingGraphs_1.10.0.tgz
Mac OS X 10.9 (Mavericks) SplicingGraphs_1.10.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SplicingGraphs/tree/release-3.2
Package Short Url http://bioconductor.org/packages/SplicingGraphs/
Package Downloads Report Download Stats

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