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

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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.

Author
D. Bindreither, M. Carlson, M. Morgan, H. Pagès
Date of publication
None
Maintainer
H. Pagès <hpages@fredhutch.org>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

Man pages

assignReads
Assign reads to the edges of a SplicingGraphs object
bubbles-methods
Compute the bubbles of a splicing graph
countReads-methods
Summarize the reads assigned to a SplicingGraphs object
plotTranscripts-methods
Plot a set of transcripts along genomic coordinates.
rsgedgesByGene-methods
Extract the reduced edges and their ranges from a...
sgedgesByGene-methods
Extract the edges and their ranges from a SplicingGraphs...
sgedges-methods
Extract the edges (and nodes) of a splicing graph
sgraph-methods
Extract a splicing graph as a plottable graph-like object
SplicingGraphs-class
SplicingGraphs objects
SplicingGraphs-package
Create, manipulate, visualize splicing graphs, and assign...
toy_data
Little helpers for quick access to the toy data included in...
TSPCsg
TSPC splicing graphs
txpath-methods
Extract the transcript paths of a splicing graph

Files in this package

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