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✨
DESCRIPTION
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)

genetics annotation datarepresentation visualization sequencing rnaseq geneexpression alternativesplicing transcription immunooncology bioconductor-package

5.72 score 2 stars 29 scripts 616 downloads 39 exports 71 dependencies

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

Target	Result	Time
bioc-checks	ERROR	278
linux-devel-x86_64	WARNING	567
source / vignettes	OK	519
linux-release-x86_64	WARNING	566
macos-release-arm64	WARNING	377
macos-oldrel-arm64	WARNING	263
windows-devel	WARNING	697
windows-release	WARNING	605
windows-oldrel	WARNING	704
wasm-release	OK	237

Exports:ASCODE2DESC assignReads bubbles countReads elementNROWS indeg intronsByTranscript isCircular<-outdeg plot plotTranscripts removeReads reportReads rsgedges rsgedgesByGene rsgedgesByTranscript rsgraph seqinfo seqnames sgedges sgedges2 sgedgesByGene sgedgesByTranscript sgnodes sgraph sgraph2 show slideshow SplicingGraphs strand toy_genes_gff toy_overlaps toy_reads_bam toy_reads_sam txpath txweight txweight<-uninformativeSSids updateObject

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue graph httr igraph IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RCurl restfulr Rgraphviz Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys vctrs XML XVector yaml

Splicing graphs and RNA-seq data

Rendered fromSplicingGraphs.Rnwusingutils::Sweave

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

Citation

Development and contributors

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 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' 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