Package: ASpli 2.17.0
Ariel Chernomoretz
ASpli: Analysis of Alternative Splicing Using RNA-Seq
Integrative pipeline for the analysis of alternative splicing using RNAseq.
Authors:
ASpli_2.17.0.tar.gz
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ASpli_2.17.0.tgz(r-4.4-any)ASpli_2.17.0.tgz(r-4.3-any)
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ASpli.pdf |ASpli.html✨
ASpli/json (API)
NEWS
| # Install 'ASpli' in R: |
| install.packages('ASpli', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ASpli-2.17.0(bioc 3.21)ASpli-2.16.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologygeneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingtimecoursernaseqgenomeannotationsequencingalignment
Last updated 2 months agofrom:5b28a12bfb. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | WARNING | Nov 29 2024 |
| R-4.5-linux | WARNING | Nov 29 2024 |
| R-4.4-win | WARNING | Nov 29 2024 |
| R-4.4-mac | WARNING | Nov 29 2024 |
| R-4.3-win | WARNING | Nov 29 2024 |
| R-4.3-mac | WARNING | Nov 29 2024 |
Exports:altPSIaltPSI<-anchorbasedanchorbased<-anchorcanchorc<-anchorjanchorj<-AsDiscoveraspliASexampleaspliBamsExampleaspliCountsExampleaspliDUexample1aspliDUexample2aspliExampleBamListaspliExampleGTFaspliFeaturesExampleaspliJunctionDUexampleaspliTargetsExamplebinbasedbinbased<-binGenomebinsDUbinsDU<-condition.ordercontainsGenesAndBinscontainsJunctionscountsbcountsb<-countse1icountse1i<-countsgcountsg<-countsie2countsie2<-countsjcountsj<-DUreportDUreport.normDUreport.offsetDUreportBinSpliceesPSIesPSI<-exportIntegratedSignalsexportSplicingReportsfeaturesbfeaturesb<-featuresgfeaturesg<-featuresjfeaturesj<-filterDUfiltersfilters<-filterSignalsgbCountsgbDUreportgenesDEgenesDE<-getConditionsintegrateSignalsirPIRirPIR<-jaltjalt<-jCountsjDUreportjesjes<-jirjir<-jointjoint<-junctionDUreportjunctionsDUjunctionsDU<-junctionsPIRjunctionsPIR<-junctionsPJUjunctionsPJU<-loadBAMlocalebasedlocalebased<-localeclocalec<-localejlocalej<-mergeBinDUASplotBinsplotGenomicRegionsrdsrdsbrdsb<-rdsgrdsg<-readCountsshowsignalssignals<-splicingReportsubsetsubsetBamssubsetTargetstargetstranscriptExonstranscriptExons<-writeAllwriteASwriteCountswriteDUwriteJDUwriteRdswriteSplicingReport
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocStylebiomaRtBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTedgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpbmcapplypillarpkgconfigplogrplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsUpSetRutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of Alternative Splicing Using RNAseq | ASpli-package ASpli |
| Accessors for ASpliAS object | altPSI altPSI<- esPSI esPSI<- irPIR irPIR<- joint joint<- junctionsPIR junctionsPIR<- junctionsPJU junctionsPJU<- |
| Deprecated functions in package 'ASpli' | ASpli-deprecated |
| Class '"ASpliAS"' | altPSI,ASpliAS-method altPSI<-,ASpliAS,data.frame-method ASpliAS ASpliAS-class esPSI,ASpliAS-method esPSI<-,ASpliAS,data.frame-method irPIR,ASpliAS-method irPIR<-,ASpliAS,data.frame-method jDUreport,ASpliAS-method joint,ASpliAS-method joint<-,ASpliAS,data.frame-method junctionsPIR,ASpliAS-method junctionsPIR<-,ASpliAS,data.frame-method junctionsPJU,ASpliAS-method junctionsPJU<-,ASpliAS,data.frame-method subset,ASpliAS-method writeAS,ASpliAS-method |
| Class '"ASpliCounts"' | ASpliCounts |
| Class '"ASpliCounts"' | AsDiscover,ASpliCounts-method ASpliCounts-class condition.order,ASpliCounts-method countsb,ASpliCounts-method countsb<-,ASpliCounts,data.frame-method countse1i,ASpliCounts-method countse1i<-,ASpliCounts,data.frame-method countsg,ASpliCounts-method countsg<-,ASpliCounts,data.frame-method countsie2,ASpliCounts-method countsie2<-,ASpliCounts,data.frame-method countsj,ASpliCounts-method countsj<-,ASpliCounts,data.frame-method DUreport,ASpliCounts-method DUreport.norm,ASpliCounts-method DUreport.offset,ASpliCounts-method DUreportBinSplice,ASpliCounts-method gbDUreport,ASpliCounts-method jCounts,ASpliCounts-method junctionDUreport,ASpliCounts-method plotBins,ASpliCounts-method rds,ASpliCounts-method rdsb,ASpliCounts-method rdsb<-,ASpliCounts,data.frame-method rdsg,ASpliCounts-method rdsg<-,ASpliCounts,data.frame-method subset,ASpliCounts-method targets,ASpliCounts-method targets<-,ASpliCounts,data.frame-method writeAll,ASpliCounts-method writeCounts,ASpliCounts-method writeRds,ASpliCounts-method |
| Class '"ASpliDU"' | ASpliDU ASpliDU-class binsDU,ASpliDU-method binsDU<-,ASpliDU-method containsGenesAndBins,ASpliDU-method containsJunctions,ASpliDU-method filterDU,ASpliDU-method genesDE,ASpliDU-method genesDE<-,ASpliDU,data.frame-method junctionsDU,ASpliDU-method junctionsDU<-,ASpliDU,data.frame-method mergeBinDUAS,ASpliDU,ASpliAS-method splicingReport,ASpliDU-method writeDU,ASpliDU-method |
| Class '"ASpliFeatures"' | ASpliFeatures-class featuresb,ASpliFeatures-method featuresb<-,ASpliFeatures,GRanges-method featuresg,ASpliFeatures-method featuresg<-,ASpliFeatures,GRangesList-method featuresj,ASpliFeatures-method featuresj<-,ASpliFeatures,GRanges-method gbCounts,ASpliFeatures-method plotGenomicRegions,ASpliFeatures-method readCounts,ASpliFeatures-method transcriptExons,ASpliFeatures-method transcriptExons<-,ASpliFeatures,GRangesList-method |
| Class '"ASpliIntegratedSignals"' | ASpliIntegratedSignals ASpliIntegratedSignals-class exportIntegratedSignals,ASpliIntegratedSignals-method filters,ASpliIntegratedSignals-method filters<-,ASpliIntegratedSignals,data.frame-method show,ASpliIntegratedSignals-method signals,ASpliIntegratedSignals-method signals<-,ASpliIntegratedSignals,data.frame-method splicingReport,ASpliIntegratedSignals-method writeIntegratedSignals,ASpliIntegratedSignals-method |
| Class '"ASpliJDU"' | anchorc,ASpliJDU-method anchorc<-,ASpliJDU,data.frame-method anchorj,ASpliJDU-method anchorj<-,ASpliJDU,data.frame-method ASpliJDU ASpliJDU-class jalt,ASpliJDU-method jalt<-,ASpliJDU,data.frame-method jDUreport,ASpliJDU-method jes,ASpliJDU-method jes<-,ASpliJDU,data.frame-method jir,ASpliJDU-method jir<-,ASpliJDU,data.frame-method localec,ASpliJDU-method localec<-,ASpliJDU,data.frame-method localej,ASpliJDU-method localej<-,ASpliJDU,data.frame-method show,ASpliJDU-method writeJDU,ASpliJDU-method |
| Class '"ASpliSplicingReport"' | anchorbased,ASpliSplicingReport-method anchorbased<-,ASpliSplicingReport,data.frame-method ASpliSplicingReport ASpliSplicingReport-class binbased,ASpliSplicingReport-method binbased<-,ASpliSplicingReport,data.frame-method exportSplicingReports,ASpliSplicingReport-method filterSignals,ASpliSplicingReport-method integrateSignals,ASpliSplicingReport-method localebased,ASpliSplicingReport-method localebased<-,ASpliSplicingReport,data.frame-method show,ASpliSplicingReport-method splicingReport,ASpliSplicingReport-method writeSplicingReport,ASpliSplicingReport-method |
| Feature coordinates extraction | binGenome |
| Feature coordinates extraction | binGenome,TxDb-method binGenome-methods |
| Accessors for ASpliCounts object | condition.order countsb countsb<- countse1i countse1i<- countsg countsg<- countsie2 countsie2<- countsj countsj<- rdsb rdsb<- rdsg rdsg<- targets |
| Accessors for ASpliDU object | binsDU binsDU<- genesDE genesDE<- junctionsDU junctionsDU<- |
| Differential gene expression and differential bin usage estimation | DUreport |
| Differential gene expression and differential bin usage estimation | DUreport.norm |
| Differential gene expression and differential bin usage estimation | DUreport.offset |
| Differential gene expression and differential bin usage estimation | DUreportBinSplice |
| Examine ASpliDU objects | containsGenesAndBins containsJunctions |
| Example Aspli objects | aspliASexample aspliBamsExample aspliCountsExample aspliDUexample1 aspliDUexample2 aspliExampleBamList aspliExampleGTF aspliFeaturesExample aspliJunctionDUexample aspliTargetsExample |
| Export integrated signals. | exportIntegratedSignals |
| Export splicing reports | exportSplicingReports |
| Accessors for ASpliFeatures object | featuresb featuresb<- featuresg featuresg<- featuresj featuresj<- transcriptExons transcriptExons<- |
| Filtering ASpliDU objects | filterDU |
| Filter signals | filterSignals |
| Summarize read overlaps | gbCounts readCounts |
| Differential gene expression and differential bin usage estimation | gbDUreport |
| Retrieve condition names from a targets data frame. | getConditions |
| Accessors for ASpliIntegratedSignals object | filters filters<- signals signals<- |
| Integrate signals | integrateSignals |
| Report PSI, PJU and PIR using experimental junctions | AsDiscover jCounts |
| Accessors for ASpliJDU object | anchorc anchorc<- anchorj anchorj<- jalt jalt<- jes jes<- jir jir<- localec localec<- localej localej<- |
| Differential junction usage estimation | jDUreport |
| Differential junction usage estimation | junctionDUreport |
| Load BAM files | loadBAM |
| Differential usage of bins and PSI/PIR. | mergeBinDUAS |
| Draw plots of gene counts, bin counts, PSI/PIR value, inclusion and exclusion junctions for selected bins. | plotBins |
| Create genomic regions coverage plots | plotGenomicRegions |
| Read density of gene and bins | rds |
| Display a summary of data contained in ASpliObjects | show,ASpliAS-method show,ASpliCounts-method show,ASpliDU-method show,ASpliFeatures-method show,ASpliMergedReports-method show-methods |
| Splicing report | splicingReport |
| Accessors for ASpliSplicingReport object | anchorbased anchorbased<- binbased binbased<- localebased localebased<- |
| Subset ASpli objects | subset subsetBams subsetTargets |
| Write results | writeAll writeAS writeCounts writeDU writeJDU writeRds writeSplicingReport |
| Write results | writeAll,ANY-method writeAS-methods writeCounts-methods writeDU-methods writeJDU-methods writeRds-methods writeSplicingReport-methods |
