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

## Documentation for package ‘SplicingGraphs’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
elementLengths-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
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