SplicingGraphs

DOI: 10.18129/B9.bioc.SplicingGraphs    

This package is for version 3.8 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: 3.8

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. Pagès

Maintainer: H. Pagès <hpages at fredhutch.org>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SplicingGraphs")

For older versions of R, please refer to the appropriate Bioconductor release.

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	AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization
Version	1.22.2
In Bioconductor since	BioC 2.12 (R-3.0) (6 years)
License	Artistic-2.0
Depends	GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7)
Imports	methods, utils, graphics, igraph, BiocGenerics, S4Vectors(>= 0.17.5), BiocParallel, IRanges(>= 2.3.21), GenomeInfoDb, GenomicRanges(>= 1.23.21), 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
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Build Report

Package Archives

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

Source Package	SplicingGraphs_1.22.2.tar.gz
Windows Binary	SplicingGraphs_1.22.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	SplicingGraphs_1.22.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SplicingGraphs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SplicingGraphs
Package Short Url	http://bioconductor.org/packages/SplicingGraphs/
Package Downloads Report	Download Stats