Package: SplicingGraphs 1.45.0

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_1.45.0.tar.gz
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SplicingGraphs_1.45.0.tgz(r-4.4-any)SplicingGraphs_1.45.0.tgz(r-4.3-any)
SplicingGraphs_1.45.0.tar.gz(r-4.5-noble)SplicingGraphs_1.45.0.tar.gz(r-4.4-noble)
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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-1.45.0(bioc 3.20)SplicingGraphs-1.44.0(bioc 3.19)

bioconductor-package

39 exports 1.00 score 72 dependencies

Last updated 2 months agofrom:d44efd649d

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 BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue graph httr igraph IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rgraphviz Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML XVector yaml zlibbioc

Splicing graphs and RNA-seq data

Rendered fromSplicingGraphs.Rnwusingutils::Sweaveon Jul 02 2024.

Last update: 2019-11-20
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 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