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

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Documentation for package ‘SplicingGraphs’ version 1.30.0

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SplicingGraphs-package Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
ASCODE2DESC Compute the bubbles of a splicing graph
assignReads Assign reads to the edges of a SplicingGraphs object
bubbles Compute the bubbles of a splicing graph
bubbles-method Compute the bubbles of a splicing graph
bubbles-methods Compute the bubbles of a splicing graph
class:GeneModel SplicingGraphs objects
class:SplicingGraphs SplicingGraphs objects
countReads Summarize the reads assigned to a SplicingGraphs object
countReads-method Summarize the reads assigned to a SplicingGraphs object
countReads-methods Summarize the reads assigned to a SplicingGraphs object
elementNROWS-method SplicingGraphs objects
GeneModel-class SplicingGraphs objects
indeg Extract the edges (and nodes) of a splicing graph
indeg-method Extract the edges (and nodes) of a splicing graph
intronsByTranscript-method Extract the edges and their ranges from a SplicingGraphs object
isCircular<--method SplicingGraphs objects
length-method SplicingGraphs objects
names-method SplicingGraphs objects
outdeg Extract the edges (and nodes) of a splicing graph
outdeg-method Extract the edges (and nodes) of a splicing graph
plot-method Extract a splicing graph as a plottable graph-like object
plotTranscripts Plot a set of transcripts along genomic coordinates.
plotTranscripts-method Plot a set of transcripts along genomic coordinates.
plotTranscripts-methods Plot a set of transcripts along genomic coordinates.
removeReads Assign reads to the edges of a SplicingGraphs object
rsgedges Extract the reduced edges and their ranges from a SplicingGraphs object
rsgedgesByGene Extract the reduced edges and their ranges from a SplicingGraphs object
rsgedgesByGene-method Extract the reduced edges and their ranges from a SplicingGraphs object
rsgedgesByGene-methods Extract the reduced edges and their ranges from a SplicingGraphs object
rsgedgesByTranscript Extract the reduced edges and their ranges from a SplicingGraphs object
rsgedgesByTranscript-method Extract the reduced edges and their ranges from a SplicingGraphs object
rsgraph Extract the reduced edges and their ranges from a SplicingGraphs object
seqinfo-method SplicingGraphs objects
seqnames-method SplicingGraphs objects
sgedges Extract the edges (and nodes) of a splicing graph
sgedges-method Extract the edges (and nodes) of a splicing graph
sgedges-methods Extract the edges (and nodes) of a splicing graph
sgedges2 Extract the reduced edges and their ranges from a SplicingGraphs object
sgedgesByGene Extract the edges and their ranges from a SplicingGraphs object
sgedgesByGene-method Extract the edges and their ranges from a SplicingGraphs object
sgedgesByGene-methods Extract the edges and their ranges from a SplicingGraphs object
sgedgesByTranscript Extract the edges and their ranges from a SplicingGraphs object
sgedgesByTranscript-method Extract the edges and their ranges from a SplicingGraphs object
sgnodes Extract the edges (and nodes) of a splicing graph
sgnodes-method Extract the edges (and nodes) of a splicing graph
sgraph Extract a splicing graph as a plottable graph-like object
sgraph-method Extract a splicing graph as a plottable graph-like object
sgraph-methods Extract a splicing graph as a plottable graph-like object
sgraph2 Extract the reduced edges and their ranges from a SplicingGraphs object
show-method SplicingGraphs objects
slideshow Extract a splicing graph as a plottable graph-like object
SplicingGraphs SplicingGraphs objects
SplicingGraphs-class SplicingGraphs objects
SplicingGraphs-method SplicingGraphs objects
strand-method SplicingGraphs objects
toy_data Little helpers for quick access to the toy data included in the 'SplicingGraphs' package
toy_genes_gff Little helpers for quick access to the toy data included in the 'SplicingGraphs' package
toy_overlaps Little helpers for quick access to the toy data included in the 'SplicingGraphs' package
toy_reads_bam Little helpers for quick access to the toy data included in the 'SplicingGraphs' package
toy_reads_sam Little helpers for quick access to the toy data included in the 'SplicingGraphs' package
TSPC TSPC splicing graphs
TSPCsg TSPC splicing graphs
txpath Extract the transcript paths of a splicing graph
txpath-method Extract the transcript paths of a splicing graph
txpath-methods Extract the transcript paths of a splicing graph
txweight Extract the transcript paths of a splicing graph
txweight-method Extract the transcript paths of a splicing graph
txweight<- Extract the transcript paths of a splicing graph
txweight<--method Extract the transcript paths of a splicing graph
uninformativeSSids Extract the reduced edges and their ranges from a SplicingGraphs object
uninformativeSSids-method Extract the reduced edges and their ranges from a SplicingGraphs object
unlist-method SplicingGraphs objects
[-method SplicingGraphs objects
[[-method SplicingGraphs objects