DOI: 10.18129/B9.bioc.SplicingGraphs  

This package is for version 3.16 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: 3.16

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")):


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PDF R Script Splicing graphs and RNA-seq data
PDF   Reference Manual


biocViews AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.38.0
In Bioconductor since BioC 2.12 (R-3.0) (10 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
Suggests igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
URL https://bioconductor.org/packages/SplicingGraphs
BugReports https://github.com/Bioconductor/SplicingGraphs/issues
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Source Package SplicingGraphs_1.38.0.tar.gz
Windows Binary SplicingGraphs_1.38.0.zip
macOS Binary (x86_64) SplicingGraphs_1.38.0.tgz
macOS Binary (arm64) SplicingGraphs_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SplicingGraphs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SplicingGraphs
Bioc Package Browser https://code.bioconductor.org/browse/SplicingGraphs/
Package Short Url https://bioconductor.org/packages/SplicingGraphs/
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