Package: SplicingGraphs 1.47.0
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:
SplicingGraphs_1.47.0.tar.gz
SplicingGraphs_1.47.0.zip(r-4.5)SplicingGraphs_1.47.0.zip(r-4.4)SplicingGraphs_1.47.0.zip(r-4.3)
SplicingGraphs_1.47.0.tgz(r-4.4-any)SplicingGraphs_1.47.0.tgz(r-4.3-any)
SplicingGraphs_1.47.0.tar.gz(r-4.5-noble)SplicingGraphs_1.47.0.tar.gz(r-4.4-noble)
SplicingGraphs_1.47.0.tgz(r-4.4-emscripten)SplicingGraphs_1.47.0.tgz(r-4.3-emscripten)
SplicingGraphs.pdf |SplicingGraphs.html✨
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-1.47.0(bioc 3.21)SplicingGraphs-1.46.0(bioc 3.20)
geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package
Last updated 2 months agofrom:2e358aaf7c. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 21 2024 |
| R-4.5-win | WARNING | Nov 21 2024 |
| R-4.5-linux | WARNING | Dec 21 2024 |
| R-4.4-win | WARNING | Nov 21 2024 |
| R-4.4-mac | WARNING | Dec 21 2024 |
| R-4.3-win | WARNING | Nov 21 2024 |
| R-4.3-mac | WARNING | Dec 21 2024 |
Exports:ASCODE2DESCassignReadsbubblescountReadselementNROWSindegintronsByTranscriptisCircular<-outdegplotplotTranscriptsremoveReadsreportReadsrsgedgesrsgedgesByGenersgedgesByTranscriptrsgraphseqinfoseqnamessgedgessgedges2sgedgesByGenesgedgesByTranscriptsgnodessgraphsgraph2showslideshowSplicingGraphsstrandtoy_genes_gfftoy_overlapstoy_reads_bamtoy_reads_samtxpathtxweighttxweight<-uninformativeSSidsupdateObject
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them | SplicingGraphs-package |
| Assign reads to the edges of a SplicingGraphs object | assignReads removeReads |
| Compute the bubbles of a splicing graph | ASCODE2DESC bubbles bubbles,ANY-method bubbles,IntegerList-method bubbles,SplicingGraphs-method bubbles-methods |
| Summarize the reads assigned to a SplicingGraphs object | countReads 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 object | rsgedges 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 graph | indeg 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 object | intronsByTranscript,SplicingGraphs-method sgedgesByGene sgedgesByGene,SplicingGraphs-method sgedgesByGene-methods sgedgesByTranscript sgedgesByTranscript,SplicingGraphs-method |
| Extract a splicing graph as a plottable graph-like object | plot,SplicingGraphs,missing-method sgraph sgraph,ANY-method sgraph,data.frame-method sgraph,DataFrame-method sgraph,igraph-method sgraph-methods slideshow |
| SplicingGraphs objects | class:GeneModel class:SplicingGraphs elementNROWS,SplicingGraphs-method GeneModel-class isCircular<-,GeneModel-method isCircular<-,SplicingGraphs-method length,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' package | toy_data toy_genes_gff toy_overlaps toy_reads_bam toy_reads_sam |
| TSPC splicing graphs | TSPC TSPCsg |
| Extract the transcript paths of a splicing graph | txpath txpath,GRangesList-method txpath,SplicingGraphs-method txpath-methods txweight txweight,SplicingGraphs-method txweight<- txweight<-,SplicingGraphs-method |
