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.

AuthorD. Bindreither, M. Carlson, M. Morgan, H. Pagès
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version1.14.0

View on Bioconductor

Functions

ASCODE2DESC Man page
assignReads Man page
bubbles Man page
bubbles,ANY-method Man page
bubbles,IntegerList-method Man page
bubbles-methods Man page
bubbles,SplicingGraphs-method Man page
class:GeneModel Man page
class:SplicingGraphs Man page
countReads Man page
countReads-methods Man page
countReads,SplicingGraphs-method Man page
elementNROWS,SplicingGraphs-method Man page
GeneModel-class Man page
indeg Man page
indeg,ANY-method Man page
indeg,DataFrame-method Man page
intronsByTranscript,SplicingGraphs-method Man page
isCircular<-,GeneModel-method Man page
isCircular<-,SplicingGraphs-method Man page
length,SplicingGraphs-method Man page
names,SplicingGraphs-method Man page
outdeg Man page
outdeg,ANY-method Man page
outdeg,DataFrame-method Man page
plot,SplicingGraphs,missing-method Man page
plotTranscripts Man page
plotTranscripts,GRangesList-method Man page
plotTranscripts-methods Man page
plotTranscripts,SplicingGraphs-method Man page
plotTranscripts,TxDb-method Man page
removeReads Man page
rsgedges Man page
rsgedgesByGene Man page
rsgedgesByGene-methods Man page
rsgedgesByGene,SplicingGraphs-method Man page
rsgedgesByTranscript Man page
rsgedgesByTranscript,SplicingGraphs-method Man page
rsgraph Man page
seqinfo,GeneModel-method Man page
seqinfo,SplicingGraphs-method Man page
seqnames,GeneModel-method Man page
seqnames,SplicingGraphs-method Man page
sgedges Man page
sgedges2 Man page
sgedgesByGene Man page
sgedgesByGene-methods Man page
sgedgesByGene,SplicingGraphs-method Man page
sgedgesByTranscript Man page
sgedgesByTranscript,SplicingGraphs-method Man page
sgedges-methods Man page
sgedges,SplicingGraphs-method Man page
sgnodes Man page
sgnodes,data.frame-method Man page
sgnodes,DataFrame-method Man page
sgnodes,IntegerList-method Man page
sgnodes,SplicingGraphs-method Man page
sgraph Man page
sgraph2 Man page
sgraph,ANY-method Man page
sgraph,data.frame-method Man page
sgraph,DataFrame-method Man page
sgraph,igraph-method Man page
sgraph-methods Man page
show,SplicingGraphs-method Man page
slideshow Man page
SplicingGraphs Man page
[,SplicingGraphs,ANY,ANY-method Man page
[[,SplicingGraphs,ANY,ANY-method Man page
SplicingGraphs-class Man page
SplicingGraphs,GRangesList-method Man page
SplicingGraphs-package Man page
SplicingGraphs,TxDb-method Man page
strand,GeneModel-method Man page
strand,SplicingGraphs-method Man page
toy_data Man page
toy_genes_gff Man page
toy_overlaps Man page
toy_reads_bam Man page
toy_reads_sam Man page
TSPC Man page
TSPCsg Man page
txpath Man page
txpath,GRangesList-method Man page
txpath-methods Man page
txpath,SplicingGraphs-method Man page
txweight Man page
txweight<- Man page
txweight<-,SplicingGraphs-method Man page
txweight,SplicingGraphs-method Man page
uninformativeSSids Man page
uninformativeSSids,ANY-method Man page
uninformativeSSids,DataFrame-method Man page
unlist,SplicingGraphs-method Man page

Files

SplicingGraphs/.Rinstignore
SplicingGraphs/DESCRIPTION
SplicingGraphs/NAMESPACE
SplicingGraphs/R
SplicingGraphs/R/SplicingGraphs-class.R SplicingGraphs/R/assignReads.R SplicingGraphs/R/bubbles-methods.R SplicingGraphs/R/countReads-methods.R SplicingGraphs/R/igraph-utils.R SplicingGraphs/R/plotTranscripts-methods.R SplicingGraphs/R/rsgedgesByGene-methods.R SplicingGraphs/R/sgedges-methods.R SplicingGraphs/R/sgedgesByGene-methods.R SplicingGraphs/R/sgraph-methods.R SplicingGraphs/R/toy_data.R SplicingGraphs/R/txpath-methods.R SplicingGraphs/R/utils.R SplicingGraphs/R/zzz.R
SplicingGraphs/TODO
SplicingGraphs/build
SplicingGraphs/build/vignette.rds
SplicingGraphs/inst
SplicingGraphs/inst/doc
SplicingGraphs/inst/doc/SplicingGraphs.R
SplicingGraphs/inst/doc/SplicingGraphs.Rnw
SplicingGraphs/inst/doc/SplicingGraphs.pdf
SplicingGraphs/inst/extdata
SplicingGraphs/inst/extdata/ASpatterns.txt
SplicingGraphs/inst/extdata/TSPCsg.rda
SplicingGraphs/inst/extdata/toy_genes.gff3
SplicingGraphs/inst/extdata/toy_overlaps.txt
SplicingGraphs/inst/extdata/toy_reads.sam
SplicingGraphs/inst/scripts
SplicingGraphs/inst/scripts/TSPC-utils.R
SplicingGraphs/inst/scripts/create-vignette-plots.R
SplicingGraphs/inst/scripts/makeTSPCsg.R
SplicingGraphs/inst/unitTests
SplicingGraphs/inst/unitTests/test_countReads-methods.R
SplicingGraphs/man
SplicingGraphs/man/SplicingGraphs-class.Rd SplicingGraphs/man/SplicingGraphs-package.Rd SplicingGraphs/man/TSPCsg.Rd SplicingGraphs/man/assignReads.Rd SplicingGraphs/man/bubbles-methods.Rd SplicingGraphs/man/countReads-methods.Rd SplicingGraphs/man/plotTranscripts-methods.Rd SplicingGraphs/man/rsgedgesByGene-methods.Rd SplicingGraphs/man/sgedges-methods.Rd SplicingGraphs/man/sgedgesByGene-methods.Rd SplicingGraphs/man/sgraph-methods.Rd SplicingGraphs/man/toy_data.Rd SplicingGraphs/man/txpath-methods.Rd
SplicingGraphs/tests
SplicingGraphs/tests/run_unitTests.R
SplicingGraphs/vignettes
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/vignettes/images
SplicingGraphs/vignettes/images/CIB3-sg.pdf
SplicingGraphs/vignettes/images/CIB3-sg2.pdf
SplicingGraphs/vignettes/images/CIB3-transcripts.pdf
SplicingGraphs/vignettes/images/ZNF813-sg.pdf
SplicingGraphs/vignettes/images/ZNF813-sg2.pdf
SplicingGraphs/vignettes/images/ZNF813-transcripts.pdf
SplicingGraphs/vignettes/precomputed_results
SplicingGraphs/vignettes/precomputed_results/sg_with_bubbles.rda
SplicingGraphs/vignettes/precomputed_results/sg_with_reads.rda

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