spliceR: Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Version 1.18.0

An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Browse man pages Browse package API and functions Browse package files

AuthorJohannes Waage <johannes.waage@gmail.com>, Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Bioconductor views AlternativeSplicing DifferentialExpression DifferentialSplicing GeneExpression Sequencing Transcription Visualization
Date of publicationNone
MaintainerJohannes Waage <johannes.waage@gmail.com>, Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
LicenseGPL (>=2)
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("spliceR")

Man pages

annotatePTC.R: PTC and NMD-sensitivity detection from assembled RNA-seq data
CDSSet: Container for coding sequence (CDS) annotation information
conditions: Returns sample condictions of an SpliceRList or an CuffSet...
dim: Retrieve the Dimensions of a SpliceRList
generateGTF: Generate GTF files for transcript visualization in genome...
getCDS: Retrieve CDS information from UCSC
prepareCuff: Prepare assembled RNA-seq data from Cufflinks for spliceR
prepareCuffExample: Prepare the Cufflinks example data
preSpliceRFilter: Filters on spliceR-lists for reduction of data sets
spliceR: Splice class detection from assembled RNA-seq data
SpliceRList: Transcript data and annotation object for spliceR
spliceRPlot: Plot venn diagrams of alternative splicing events
tools: Returns the transcript or exon GRanges from a SpliceRList...
topIsoShift: Returns top transcripts in terms of isoform switching
totalNumberOfAS: Returns total number of alternative splicing events

Functions

CDSSet Man page Source code
CDSSet-class Man page
SpliceRList Man page Source code
SpliceRList-class Man page
annotatePTC Man page Source code
conditions Man page Source code
determineAStypeOverlap Source code
determineLeftOverlappingAStype Source code
determineNonOverlappingAStype Source code
determineRightOverlappingAStype Source code
dim.SpliceRList Man page Source code
evaluateCounter Source code
exons Man page Source code
filterExpressedGenes Source code
filterExpressedIso Source code
filterIsoClassCode Source code
filterOKGenes Source code
filterOKIso Source code
filterPTC Source code
filterSigGenes Source code
filterSigIso Source code
filterSingleExonIsoAll Source code
filterSingleIsoform Source code
findIdenticalExons Source code
findOverlap Source code
findOverlappingExons Source code
generateGTF Man page Source code
getCDS Man page Source code
getIntersectVennData Source code
getMajorIsoCuffDB Source code
getPreRNA Source code
length.SpliceRList Man page Source code
preSpliceRFilter Man page Source code
prepareCuff Man page Source code
prepareCuffExample Man page Source code
spliceR Man page Source code
spliceRPlot Man page Source code
topIsoShift Man page Source code
totalNumberOfAS Man page Source code
transcripts Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/CDSSet.R
R/SpliceRList.R
R/annotatePTC.R
R/classes.R
R/generateGTF.R
R/getCDS.R
R/prepareCuff.R
R/spliceR.R
R/spliceR_aux.R
R/spliceRplot.R
R/tools.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/spliceR.R
inst/doc/spliceR.Rnw
inst/doc/spliceR.pdf
man
man/CDSSet.Rd
man/SpliceRList.Rd
man/annotatePTC.R.Rd
man/conditions.Rd
man/dim.Rd
man/generateGTF.Rd
man/getCDS.Rd
man/preSpliceRFilter.Rd
man/prepareCuff.Rd
man/prepareCuffExample.Rd
man/spliceR.Rd
man/spliceRPlot.Rd
man/tools.Rd
man/topIsoShift.Rd
man/totalNumberOfAS.Rd
src
src/utils.c
vignettes
vignettes/spliceR.Rnw
spliceR documentation built on May 20, 2017, 10:21 p.m.