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.

AuthorDiana Low
Date of publicationNone
MaintainerDiana Low <dlow@imcb.a-star.edu.sg>
LicenseGPL-2
Version1.0.0

View on Bioconductor

Functions

addEnsemblAnnotation Man page
callPrimer3 Man page
checkPrimer Man page
compatible_cds Man page
compatible_tx 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
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

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