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

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

Author
Johannes Waage <johannes.waage@gmail.com>, Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date of publication
None
Maintainer
Johannes Waage <johannes.waage@gmail.com>, Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
License
GPL (>=2)
Version
1.16.0

View on Bioconductor

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

Files in this package

spliceR/DESCRIPTION
spliceR/NAMESPACE
spliceR/R
spliceR/R/CDSSet.R
spliceR/R/SpliceRList.R
spliceR/R/annotatePTC.R
spliceR/R/classes.R
spliceR/R/generateGTF.R
spliceR/R/getCDS.R
spliceR/R/prepareCuff.R
spliceR/R/spliceR.R
spliceR/R/spliceR_aux.R
spliceR/R/spliceRplot.R
spliceR/R/tools.R
spliceR/build
spliceR/build/vignette.rds
spliceR/inst
spliceR/inst/NEWS.Rd
spliceR/inst/doc
spliceR/inst/doc/spliceR.R
spliceR/inst/doc/spliceR.Rnw
spliceR/inst/doc/spliceR.pdf
spliceR/man
spliceR/man/CDSSet.Rd
spliceR/man/SpliceRList.Rd
spliceR/man/annotatePTC.R.Rd
spliceR/man/conditions.Rd
spliceR/man/dim.Rd
spliceR/man/generateGTF.Rd
spliceR/man/getCDS.Rd
spliceR/man/preSpliceRFilter.Rd
spliceR/man/prepareCuff.Rd
spliceR/man/prepareCuffExample.Rd
spliceR/man/spliceR.Rd
spliceR/man/spliceRPlot.Rd
spliceR/man/tools.Rd
spliceR/man/topIsoShift.Rd
spliceR/man/totalNumberOfAS.Rd
spliceR/src
spliceR/src/utils.c
spliceR/vignettes
spliceR/vignettes/spliceR.Rnw