SplicingGraphs

DOI: 10.18129/B9.bioc.SplicingGraphs    

This is the development version of SplicingGraphs; for the stable release version, see SplicingGraphs.

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

Bioconductor version: Development (3.13)

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.on.github at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.31.1
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 https://bioconductor.org/packages/SplicingGraphs
BugReports https://github.com/Bioconductor/SplicingGraphs/issues
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_1.31.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) SplicingGraphs_1.31.1.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

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