RDocumentation
Moon
Learn R
Search all packages and functions
JunctionSeq (version 1.2.4)
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
Description
A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.
Copy Link
Copy
Link to current version
Version
Version
1.2.4
Down Chevron
Version
1.2.4
License
file LICENSE
Maintainer
Stephen Hartley
Last Published
January 1st, 1970
Functions in JunctionSeq (1.2.4)
Search functions
defaultColorList
JunctionSeq Color Parameters
JunctionSeqCountSet-class
Class
"JunctionSeqCountSet"
estimateJunctionSeqDispersions
JunctionSeq Dispersion Estimation
writeBedTrack
Write splice junction browser tracks
fitJunctionSeqDispersionFunction
Fit Shared Dispersion Function
buildAllPlotsForGene
Create and save one or more JunctionSeq expression plots.
testForDiffUsage
Test Junctions for Differential Junction Usage
runJunctionSeqAnalyses
Run a JunctionSeq analysis.
plotJunctionSeqResultsForGene
Generate a JunctionSeq expression plot.
plotMA
Generate a MA-Plot
buildAllPlots
Create and save a full battery of JunctionSeq expression plots.
plotDispEsts
Plot Fitted and Test-wise Dispersion
readAnnotationData
Read junctionSeq annotation files produced by QoRTs.
readJunctionSeqCounts
Read junctionSeq count files
writeCompleteResults
Produce output data files, given annotation files and DEXSeq exonCountSet object and DEXSeq results data.
estimateJunctionSeqSizeFactors
Estimate Size Factors
estimateEffectSizes
Estimate Effect Sizes, parameter estimates, etc.