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SplicingGraphs

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


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
Splicing graphs and RNA-seq data PDF R Script
Reference Manual PDF

Details

biocViews AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.42.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
System Requirements
URL https://bioconductor.org/packages/SplicingGraphs
Bug Reports https://github.com/Bioconductor/SplicingGraphs/issues
See More
Suggests igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit
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Package Archives

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

Source Package SplicingGraphs_1.42.0.tar.gz
Windows Binary SplicingGraphs_1.42.0.zip
macOS Binary (x86_64) SplicingGraphs_1.42.0.tgz
macOS Binary (arm64) SplicingGraphs_1.42.0.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/
Package Downloads Report Download Stats