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 |