SplicingGraphs

DOI: 10.18129/B9.bioc.SplicingGraphs    

This package is for version 3.9 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: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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 1.24.0
In Bioconductor since BioC 2.12 (R-3.0) (6.5 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(>= 2.3.21), 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
Links To Me
Build Report  

Package Archives

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

Source Package SplicingGraphs_1.24.0.tar.gz
Windows Binary SplicingGraphs_1.24.0.zip
Mac OS X 10.11 (El Capitan) SplicingGraphs_1.24.0.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

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