Learn R Programming
⚠️There's a newer version (1.12.0) of this package.Take me there.

SplicingGraphs (version 1.10.0)

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

Description

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.

Copy Link

Version

Version

1.10.0

License

Artistic-2.0

Maintainer

H Pages

Last Published

February 15th, 2017

Functions in SplicingGraphs (1.10.0)

bubbles-methods

Compute the bubbles of a splicing graph
sgedges-methods

Extract the edges (and nodes) of a splicing graph
assignReads

Assign reads to the edges of a SplicingGraphs object
SplicingGraphs-class

SplicingGraphs objects
SplicingGraphs-package

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

Extract the edges and their ranges from a SplicingGraphs object
plotTranscripts-methods

Plot a set of transcripts along genomic coordinates.
rsgedgesByGene-methods

Extract the reduced edges and their ranges from a SplicingGraphs object
sgraph-methods

Extract a splicing graph as a plottable graph-like object
countReads-methods

Summarize the reads assigned to a SplicingGraphs object
txpath-methods

Extract the transcript paths of a splicing graph
toy_data

Little helpers for quick access to the toy data included in the SplicingGraphs package
TSPCsg

TSPC splicing graphs