SplicingGraphs

DOI: 10.18129/B9.bioc.SplicingGraphs    

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

Bioconductor version: Release (3.11)

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 "4.0") 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	1.28.0
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 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(>= 2.21.2), 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
Links To Me
Build Report

Package Archives

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

Source Package	SplicingGraphs_1.28.0.tar.gz
Windows Binary	SplicingGraphs_1.28.0.zip
macOS 10.13 (High Sierra)	SplicingGraphs_1.28.0.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	https://bioconductor.org/packages/SplicingGraphs/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive