Package: GeneStructureTools 1.27.0

Beth Signal

GeneStructureTools: Tools for spliced gene structure manipulation and analysis

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

Authors:Beth Signal

GeneStructureTools_1.27.0.tar.gz
GeneStructureTools_1.27.0.zip(r-4.5)GeneStructureTools_1.27.0.zip(r-4.4)GeneStructureTools_1.27.0.zip(r-4.3)
GeneStructureTools_1.27.0.tgz(r-4.4-any)GeneStructureTools_1.27.0.tgz(r-4.3-any)
GeneStructureTools_1.27.0.tar.gz(r-4.5-noble)GeneStructureTools_1.27.0.tar.gz(r-4.4-noble)
GeneStructureTools_1.27.0.tgz(r-4.4-emscripten)GeneStructureTools_1.27.0.tgz(r-4.3-emscripten)
GeneStructureTools.pdf |GeneStructureTools.html✨
GeneStructureTools/json (API)
NEWS

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

Peer review:

On BioConductor:GeneStructureTools-1.27.0(bioc 3.21)GeneStructureTools-1.26.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysoftwaredifferentialsplicingfunctionalpredictiontranscriptomicsalternativesplicingrnaseq

3.32 score 21 scripts 260 downloads 40 exports 150 dependencies

Last updated 23 days agofrom:001986bed3. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 14 2024
R-4.5-winWARNINGNov 14 2024
R-4.5-linuxWARNINGNov 14 2024
R-4.4-winWARNINGNov 14 2024
R-4.4-macWARNINGNov 14 2024
R-4.3-winWARNINGNov 14 2024
R-4.3-macWARNINGNov 14 2024

Exports:addBroadTypesaddIntronInTranscriptalternativeIntronUsageannotateGeneModelattrChangeAltSplicedcoordinatesDEXSeqIdsToGeneIdsdiffSplicingResultsexonsToTranscriptsfilterGtfOverlapfilterWhippetEventsfindDEXexonTypefindExonContainingTranscriptsfindIntronContainingTranscriptsfindJunctionPairsformatWhippetEventsgetOrfsgetUOrfsjunctionsleafcutterTranscriptChangeSummarymakeGeneModelmaxLocationorfDifforfSimilarityoverlapTypesreadCountsreadWhippetDataSetreadWhippetDIFFfilesreadWhippetJNCfilesreadWhippetPSIfilesremoveDuplicateTranscriptsremoveSameExonremoveVersionreorderExonNumbersreplaceJunctionskipExonInTranscriptsummariseExonTypestranscriptChangeSummaryUTR2UTR53whippetTranscriptChangeSummary

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomeBSgenome.Mmusculus.UCSC.mm10bslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringdiststringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Change transcript biotypes to a broader setaddBroadTypes
Add a retained intron to the transcripts it is skipped byaddIntronInTranscript
Create transcripts with alternative intron usagealternativeIntronUsage
Annotate a GRanges gene model with ORF boundries for visualisation with GvizannotateGeneModel
Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcriptsattrChangeAltSpliced
Method coordinatescoordinates coordinates,whippetDataSet-method
Convert DEXSeq ids to gene idsDEXSeqIdsToGeneIds
Method diffSplicingResultsdiffSplicingResults diffSplicingResults,whippetDataSet-method
Convert an exon-level gtf annotation to a transcript-level gtf annotationexonsToTranscripts
Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTRfilterGtfOverlap
Filter out significant events from a whippet diff comparisonfilterWhippetEvents
Find a DEXSeq exons' biotypefindDEXexonType
Given the location of a whole spliced in exon, find transcripts which can splice out this exonfindExonContainingTranscripts
Given the location of a whole retained intron, find transcripts which splice out this intronfindIntronContainingTranscripts
Find alternative junctions for Whippet alternative splicing eventsfindJunctionPairs
Format Whippet co-ordinates as a GRanges objectformatWhippetEvents
Get open reading frames for transcriptsgetOrfs
Get upstream open reading frames for transcripts with annotated main ORFsgetUOrfs
Method junctionsjunctions junctions,whippetDataSet-method
Compare open reading frames for whippet differentially spliced eventsleafcutterTranscriptChangeSummary
Convert GRanges gene model to data.frame for visualisation with GvizmakeGeneModel
Find the largest distance between two vectors of numbers Helper function for get_orfsmaxLocation
Evaluate changes to ORFs caused by alternative splicingorfDiff
calculate percentage of orfB contained in orfAorfSimilarity
Annotate introns and exonic parts by overlaping exon biotypeoverlapTypes
Method readCountsreadCounts readCounts,whippetDataSet-method
Import whippet results files as a whippetDataSetreadWhippetDataSet
Read in a list of whippet .diff.gz files and format as a data.framereadWhippetDIFFfiles
Read in a list of whippet .jnc.gz files and format as a GRanges objectreadWhippetJNCfiles
Read in a list of whippet .psi.gz files and format as a data.framereadWhippetPSIfiles
Remove transcript duplicatesremoveDuplicateTranscripts
Remove exon duplicatesremoveSameExon
Remove version number from ensembl gene/transcript idsremoveVersion
Reorder the exon numbers in a gtf annotationreorderExonNumbers
Find transcripts containing/overlapping junctions and replace them with alternative junctionsreplaceJunction
Remove and include a skipped exon from the transcripts it overlapsskipExonInTranscript
Summarise exon biotypes to broader categoriessummariseExonTypes
Compare open reading frames for two sets of paired transcriptstranscriptChangeSummary
Annotate UTRs from Gencode GTF as 5' or 3'UTR2UTR53
Class whippetDataSetwhippetDataSet-class
Compare open reading frames for whippet differentially spliced eventswhippetTranscriptChangeSummary