Package: SPLINTER 1.38.0

Diana Low

SPLINTER: Splice Interpreter of Transcripts

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.

Authors:Diana Low [aut, cre]

SPLINTER_1.38.0.tar.gz
SPLINTER_1.38.0.zip(r-4.7)SPLINTER_1.38.0.zip(r-4.6)SPLINTER_1.38.0.zip(r-4.5)
SPLINTER_1.38.0.tgz(r-4.6-any)SPLINTER_1.38.0.tgz(r-4.5-any)
SPLINTER_1.38.0.tar.gz(r-4.7-any)SPLINTER_1.38.0.tar.gz(r-4.6-any)
SPLINTER_1.38.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SPLINTER/json (API)
NEWS

# Install 'SPLINTER' in R:
install.packages('SPLINTER', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dianalow/splinter/issues

Datasets:

On BioConductor:SPLINTER-1.39.0(bioc 3.24)SPLINTER-1.38.0(bioc 3.23)

immunooncologygeneexpressionrnaseqvisualizationalternativesplicing

4.18 score 1 scripts 352 downloads 16 mentions 25 exports 147 dependencies

Last updated from:abff26a9dd (on RELEASE_3_23). Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING229
linux-devel-x86_64WARNING507
source / vignettesERROR427
linux-release-x86_64WARNING540
macos-release-arm64WARNING441
macos-oldrel-arm64WARNING268
windows-develWARNING413
windows-releaseWARNING383
windows-oldrelWARNING435
wasm-releaseOK227

Exports:addEnsemblAnnotationannotateEventscallPrimer3checkPrimereventOutcomeCompareeventOutcomeTranslateeventPlotextendROIextractSpliceEventsextractSpliceSitesfindCompatibleEventsfindCompatibleExonfindTXgetPCRsizesgetRegionDNAinsertRegionmakeROImakeUniqueIDsplot_seqlogopsiPlotremoveRegionshapiroAcceptorshapiroDensityshapiroDonorsplitPCRhit

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomeBSgenome.Mmusculus.UCSC.mm9bslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegoogleVisgridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseqLogosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
acceptor.macceptor.m
addEnsemblAnnotationaddEnsemblAnnotation
annotateEventsannotateEvents
callPrimer3callPrimer3
checkPrimercheckPrimer
compatible_cdscompatible_cds
compatible_txcompatible_tx
donor.mdonor.m
eventOutcomeCompareeventOutcomeCompare
eventOutcomeTranslateeventOutcomeTranslate
eventPloteventPlot
extendROIextendROI
extractSpliceEventsextractSpliceEvents
extractSpliceSitesextractSpliceSites
findCompatibleEventsfindCompatibleEvents
findCompatibleExonfindCompatibleExon
findTXfindTX
getPCRsizesgetPCRsizes
getRegionDNAgetRegionDNA
insertRegioninsertRegion
makeROImakeROI
makeUniqueIDsmakeUniqueIDs
pcr_result1pcr_result1
plotting sequence logoplot_seqlogo
primersprimers
psiPlotpsiPlot
region_minus_exonregion_minus_exon
removeRegionremoveRegion
roiroi
shapiroAcceptorshapiroAcceptor
shapiroDensityshapiroDensity
shapiroDonorshapiroDonor
splice_datasplice_data
splice_fastasplice_fasta
splitPCRhitsplitPCRhit
thecdsthecds
theexonstheexons
valid_cdsvalid_cds
valid_txvalid_tx