Package: SplicingGraphs 1.53.0

H. Pagès

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

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.

Authors:D. Bindreither, M. Carlson, M. Morgan, H. Pagès

SplicingGraphs_1.53.0.tar.gz
SplicingGraphs_1.53.0.zip(r-4.7)SplicingGraphs_1.53.0.zip(r-4.6)SplicingGraphs_1.53.0.zip(r-4.5)
SplicingGraphs_1.53.0.tgz(r-4.6-any)SplicingGraphs_1.53.0.tgz(r-4.5-any)
SplicingGraphs_1.53.0.tar.gz(r-4.7-any)SplicingGraphs_1.53.0.tar.gz(r-4.6-any)
SplicingGraphs_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SplicingGraphs/json (API)

# Install 'SplicingGraphs' in R:
install.packages('SplicingGraphs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/splicinggraphs/issues

On BioConductor:SplicingGraphs-1.53.0(bioc 3.24)SplicingGraphs-1.52.0(bioc 3.23)

geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package

5.58 score 2 stars 21 scripts 578 downloads 39 exports 71 dependencies

Last updated from:0d0f030b8f. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR259
linux-devel-x86_64WARNING567
source / vignettesOK525
linux-release-x86_64WARNING525
macos-release-arm64WARNING314
macos-oldrel-arm64WARNING283
windows-develWARNING968
windows-releaseWARNING653
windows-oldrelWARNING1073
wasm-releaseOK216

Exports:ASCODE2DESCassignReadsbubblescountReadselementNROWSindegintronsByTranscriptisCircular<-outdegplotplotTranscriptsremoveReadsreportReadsrsgedgesrsgedgesByGenersgedgesByTranscriptrsgraphseqinfoseqnamessgedgessgedges2sgedgesByGenesgedgesByTranscriptsgnodessgraphsgraph2showslideshowSplicingGraphsstrandtoy_genes_gfftoy_overlapstoy_reads_bamtoy_reads_samtxpathtxweighttxweight<-uninformativeSSidsupdateObject

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLXVectoryaml

Splicing graphs and RNA-seq data

Rendered fromSplicingGraphs.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2025-11-02
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to themSplicingGraphs-package
Assign reads to the edges of a SplicingGraphs objectassignReads removeReads
Compute the bubbles of a splicing graphASCODE2DESC bubbles bubbles,ANY-method bubbles,IntegerList-method bubbles,SplicingGraphs-method bubbles-methods
Summarize the reads assigned to a SplicingGraphs objectcountReads countReads,SplicingGraphs-method countReads-methods
Plot a set of transcripts along genomic coordinates.plotTranscripts plotTranscripts,GRangesList-method plotTranscripts,SplicingGraphs-method plotTranscripts,TxDb-method plotTranscripts-methods
Extract the reduced edges and their ranges from a SplicingGraphs objectrsgedges rsgedgesByGene rsgedgesByGene,SplicingGraphs-method rsgedgesByGene-methods rsgedgesByTranscript rsgedgesByTranscript,SplicingGraphs-method rsgraph sgedges2 sgraph2 uninformativeSSids uninformativeSSids,ANY-method uninformativeSSids,DataFrame-method
Extract the edges (and nodes) of a splicing graphindeg indeg,ANY-method indeg,DataFrame-method outdeg outdeg,ANY-method outdeg,DataFrame-method sgedges sgedges,SplicingGraphs-method sgedges-methods sgnodes sgnodes,data.frame-method sgnodes,DataFrame-method sgnodes,IntegerList-method sgnodes,SplicingGraphs-method
Extract the edges and their ranges from a SplicingGraphs objectintronsByTranscript,SplicingGraphs-method sgedgesByGene sgedgesByGene,SplicingGraphs-method sgedgesByGene-methods sgedgesByTranscript sgedgesByTranscript,SplicingGraphs-method
Extract a splicing graph as a plottable graph-like objectplot,SplicingGraphs,missing-method sgraph sgraph,ANY-method sgraph,data.frame-method sgraph,DataFrame-method sgraph,igraph-method sgraph-methods slideshow
SplicingGraphs objectsclass:GeneModel class:SplicingGraphs elementNROWS,SplicingGraphs-method GeneModel-class isCircular<-,GeneModel-method isCircular<-,SplicingGraphs-method length,SplicingGraphs-method lengths,SplicingGraphs-method names,SplicingGraphs-method seqinfo,GeneModel-method seqinfo,SplicingGraphs-method seqnames,GeneModel-method seqnames,SplicingGraphs-method show,SplicingGraphs-method SplicingGraphs SplicingGraphs,GRangesList-method SplicingGraphs,TxDb-method SplicingGraphs-class strand,GeneModel-method strand,SplicingGraphs-method unlist,SplicingGraphs-method updateObject,SplicingGraphs-method [,SplicingGraphs,ANY,ANY,ANY-method [[,SplicingGraphs,ANY,ANY-method
Little helpers for quick access to the toy data included in the 'SplicingGraphs' packagetoy_data toy_genes_gff toy_overlaps toy_reads_bam toy_reads_sam
TSPC splicing graphsTSPC TSPCsg
Extract the transcript paths of a splicing graphtxpath txpath,GRangesList-method txpath,SplicingGraphs-method txpath-methods txweight txweight,SplicingGraphs-method txweight<- txweight<-,SplicingGraphs-method