SPLINTER: Splice Interpreter Of Transcripts

SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SPLINTER")
AuthorDiana Low
Bioconductor views AlternativeSplicing GeneExpression RNASeq Visualization
Date of publicationNone
MaintainerDiana Low <dlow@imcb.a-star.edu.sg>
LicenseGPL-2
Version1.2.0

View on Bioconductor

Functions

acceptor.m Man page
addEnsemblAnnotation Man page
callPrimer3 Man page
checkPrimer Man page
compatible_cds Man page
compatible_tx Man page
donor.m Man page
eventOutcomeCompare Man page
eventOutcomeTranslate Man page
eventPlot Man page
extendROI Man page
extractSpliceEvents Man page
extractSpliceSites Man page
findCompatibleEvents Man page
findCompatibleExon Man page
findExactOverlaps Man page
findTermination Man page
findTX Man page
getPCRsizes Man page
getRegionDNA Man page
insertRegion Man page
makeROI Man page
makeUniqueIDs Man page
matchExons Man page
metaremove Man page
pcr_result1 Man page
plot_seqlogo Man page
primers Man page
psiPlot Man page
region_minus_exon Man page
removeRegion Man page
remvalue Man page
roi Man page
shapiroAcceptor Man page
shapiroDensity Man page
shapiroDonor Man page
splice_data Man page
splice_fasta Man page
splitPCRhit Man page
thecds Man page
theexons Man page
valid_cds Man page
valid_tx Man page

Files

DESCRIPTION
NAMESPACE
NEWS
NEWS.md
R
R/main_splinter.R R/primerpcr.R
SPLINTER.Rproj
build
build/vignette.rds
data
data/acceptor.m.rda
data/compatible_cds.rda
data/compatible_tx.rda
data/donor.m.rda
data/pcr_result1.rda
data/primers.rda
data/region_minus_exon.rda
data/roi.rda
data/splice_data.rda
data/splice_fasta.rda
data/thecds.rda
data/theexons.rda
data/valid_cds.rda
data/valid_tx.rda
inst
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rmd
inst/doc/vignette.pdf
inst/extdata
inst/extdata/Mus_musculus.Ensembl.NCBIM37.65.partial.gtf
inst/extdata/mt_chr14.bam
inst/extdata/mt_chr14.bam.bai
inst/extdata/skipped_exons.txt
inst/extdata/wt_chr14.bam
inst/extdata/wt_chr14.bam.bai
man
man/acceptor.m.Rd man/addEnsemblAnnotation.Rd man/callPrimer3.Rd man/checkPrimer.Rd man/compatible_cds.Rd man/compatible_tx.Rd man/donor.m.Rd man/eventOutcomeCompare.Rd man/eventOutcomeTranslate.Rd man/eventPlot.Rd man/extendROI.Rd man/extractSpliceEvents.Rd man/extractSpliceSites.Rd man/findCompatibleEvents.Rd man/findCompatibleExon.Rd man/findExactOverlaps.Rd man/findTX.Rd man/findTermination.Rd man/getPCRsizes.Rd man/getRegionDNA.Rd man/insertRegion.Rd man/makeROI.Rd man/makeUniqueIDs.Rd man/matchExons.Rd man/metaremove.Rd man/pcr_result1.Rd man/plot_seqlogo.Rd man/primers.Rd man/psiPlot.Rd man/region_minus_exon.Rd man/removeRegion.Rd man/remvalue.Rd man/roi.Rd man/shapiroAcceptor.Rd man/shapiroDensity.Rd man/shapiroDonor.Rd man/splice_data.Rd man/splice_fasta.Rd man/splitPCRhit.Rd man/thecds.Rd man/theexons.Rd man/valid_cds.Rd man/valid_tx.Rd
vignettes
vignettes/vignette.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.