Package: SPLINTER 1.33.0

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_1.33.0.tar.gz
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SPLINTER.pdf |SPLINTER.html✨
SPLINTER/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:SPLINTER-1.33.0(bioc 3.21)SPLINTER-1.32.0(bioc 3.20)

immunooncologygeneexpressionrnaseqvisualizationalternativesplicing

5.30 score 1 scripts 201 downloads 16 mentions 25 exports 152 dependencies

Last updated 23 days agofrom:15c42109e1. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:addEnsemblAnnotationannotateEventscallPrimer3checkPrimereventOutcomeCompareeventOutcomeTranslateeventPlotextendROIextractSpliceEventsextractSpliceSitesfindCompatibleEventsfindCompatibleExonfindTXgetPCRsizesgetRegionDNAinsertRegionmakeROImakeUniqueIDsplot_seqlogopsiPlotremoveRegionshapiroAcceptorshapiroDensityshapiroDonorsplitPCRhit

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomeBSgenome.Mmusculus.UCSC.mm9bslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegoogleVisgridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesseqLogosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

SPLINTER

Diana Low

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-03-27
Started: 2016-10-07

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