JunctionSeq: JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.

Author
Stephen Hartley [aut, cre] (PhD), Simon Anders [cph], Alejandro Reyes [cph]
Date of publication
None
Maintainer
Stephen Hartley <JunctionSeq-contact@list.nih.gov>
License
file LICENSE
Version
1.4.0
URLs

View on Bioconductor

Man pages

buildAllPlots
Create and save a full battery of JunctionSeq expression...
buildAllPlotsForGene
Create and save one or more JunctionSeq expression plots.
defaultColorList
JunctionSeq Color Parameters
estimateEffectSizes
Estimate Effect Sizes, parameter estimates, etc.
estimateJunctionSeqDispersions
JunctionSeq Dispersion Estimation
estimateJunctionSeqSizeFactors
Estimate Size Factors
fitJunctionSeqDispersionFunction
Fit Shared Dispersion Function
JunctionSeqCountSet-class
Class '"JunctionSeqCountSet"'
plotDispEsts
Plot Fitted and Test-wise Dispersion
plotJunctionSeqResultsForGene
Generate a JunctionSeq expression plot.
plotMA
Generate a MA-Plot
readAnnotationData
Read junctionSeq annotation files produced by QoRTs.
readJunctionSeqCounts
Read junctionSeq count files
runJunctionSeqAnalyses
Run a JunctionSeq analysis.
testForDiffUsage
Test Junctions for Differential Junction Usage
writeBedTrack
Write splice junction browser tracks
writeCompleteResults
Produce output data files, given annotation files and DEXSeq...

Files in this package

JunctionSeq/DESCRIPTION
JunctionSeq/LICENSE
JunctionSeq/NAMESPACE
JunctionSeq/NEWS
JunctionSeq/R
JunctionSeq/R/00.minor.utils.R
JunctionSeq/R/03.AllClasses.R
JunctionSeq/R/DESeq2.adapted.cpp.wrappers.R
JunctionSeq/R/adapted.functions.R
JunctionSeq/R/file.output.R
JunctionSeq/R/func.R
JunctionSeq/R/internal.func.R
JunctionSeq/R/main.analysis.R
JunctionSeq/R/main.plotAlt.R
JunctionSeq/R/main.plotGenes.R
JunctionSeq/R/plotting.helpers.R
JunctionSeq/build
JunctionSeq/build/vignette.rds
JunctionSeq/inst
JunctionSeq/inst/CITATION
JunctionSeq/inst/doc
JunctionSeq/inst/doc/JunctionSeq.Rnw
JunctionSeq/inst/doc/JunctionSeq.pdf
JunctionSeq/inst/doc/gpl.v3.txt
JunctionSeq/inst/extdata
JunctionSeq/inst/extdata/styles.css
JunctionSeq/man
JunctionSeq/man/JunctionSeqCountSet-class.Rd
JunctionSeq/man/buildAllPlots.Rd
JunctionSeq/man/buildAllPlotsForGene.Rd
JunctionSeq/man/defaultColorList.Rd
JunctionSeq/man/estimateEffectSizes.Rd
JunctionSeq/man/estimateJunctionSeqDispersions.Rd
JunctionSeq/man/estimateJunctionSeqSizeFactors.Rd
JunctionSeq/man/fitJunctionSeqDispersionFunction.Rd
JunctionSeq/man/plotDispEsts.Rd
JunctionSeq/man/plotJunctionSeqResultsForGene.Rd
JunctionSeq/man/plotMA.Rd
JunctionSeq/man/readAnnotationData.Rd
JunctionSeq/man/readJunctionSeqCounts.Rd
JunctionSeq/man/runJunctionSeqAnalyses.Rd
JunctionSeq/man/testForDiffUsage.Rd
JunctionSeq/man/writeBedTrack.Rd
JunctionSeq/man/writeCompleteResults.Rd
JunctionSeq/vignettes
JunctionSeq/vignettes/JunctionSeq.Rnw
JunctionSeq/vignettes/JunctionSeq.bib
JunctionSeq/vignettes/figs
JunctionSeq/vignettes/figs/DAY-wiggle.png
JunctionSeq/vignettes/figs/SHAM1_RG1-wiggle.png
JunctionSeq/vignettes/figs/final.png
JunctionSeq/vignettes/figs/fullMultiWig.png
JunctionSeq/vignettes/figs/junctions.png