SPLINTER: Splice Interpreter Of Transcripts

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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.

Author
Diana Low
Date of publication
None
Maintainer
Diana Low <dlow@imcb.a-star.edu.sg>
License
GPL-2
Version
1.0.0

View on Bioconductor

Man pages

addEnsemblAnnotation
addEnsemblAnnotation
callPrimer3
callPrimer3
checkPrimer
checkPrimer
compatible_cds
compatible_cds
compatible_tx
compatible_tx
eventOutcomeCompare
eventOutcomeCompare
eventOutcomeTranslate
eventOutcomeTranslate
eventPlot
eventPlot
extendROI
extendROI
extractSpliceEvents
extractSpliceEvents
extractSpliceSites
extractSpliceSites
findCompatibleEvents
findCompatibleEvents
findCompatibleExon
findCompatibleExon
findExactOverlaps
findExactOverlaps
findTermination
findTermination
findTX
findTX
getPCRsizes
getPCRsizes
getRegionDNA
getRegionDNA
insertRegion
insertRegion
makeROI
makeROI
makeUniqueIDs
makeUniqueIDs
matchExons
matchExons
metaremove
metaremove
pcr_result1
pcr_result1
plot_seqlogo
plotting sequence logo
primers
primers
psiPlot
psiPlot
region_minus_exon
region_minus_exon
removeRegion
removeRegion
remvalue
remvalue
roi
roi
splice_data
splice_data
splice_fasta
splice_fasta
splitPCRhit
splitPCRhit
thecds
thecds
theexons
theexons
valid_cds
valid_cds
valid_tx
valid_tx

Files in this package

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