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 <email@example.com>|
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