Package: ASpli 2.23.0

Ariel Chernomoretz

ASpli: Analysis of Alternative Splicing Using RNA-Seq

Integrative pipeline for the analysis of alternative splicing using RNAseq.

Authors:Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky and Ariel Chernomoretz

ASpli_2.23.0.tar.gz
ASpli_2.23.0.zip(r-4.7)ASpli_2.23.0.zip(r-4.6)ASpli_2.23.0.zip(r-4.5)
ASpli_2.23.0.tgz(r-4.6-any)ASpli_2.23.0.tgz(r-4.5-any)
ASpli_2.23.0.tar.gz(r-4.7-any)ASpli_2.23.0.tar.gz(r-4.6-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ASpli/json (API)

# Install 'ASpli' in R:

install.packages('ASpli', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ASpli-2.23.0(bioc 3.24)ASpli-2.22.0(bioc 3.23)

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

immunooncology geneexpression transcription alternativesplicing coverage differentialexpression differentialsplicing timecourse rnaseq genomeannotation sequencing alignment

5.10 score 1 packages 53 scripts 4 mentions 113 exports 160 dependencies

Last updated from:ccb8e28be3. Checks:3 ERROR, 2 OK, 5 WARNING. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	261
linux-devel-x86_64	ERROR	533
source / vignettes	OK	399
linux-release-x86_64	WARNING	969
macos-release-arm64	WARNING	507
macos-oldrel-arm64	WARNING	513
windows-devel	ERROR	373
windows-release	WARNING	891
windows-oldrel	WARNING	858
wasm-release	OK	236

Exports:altPSI altPSI<-anchorbased anchorbased<-anchorc anchorc<-anchorj anchorj<-AsDiscover aspliASexample aspliBamsExample aspliCountsExample aspliDUexample1 aspliDUexample2 aspliExampleBamList aspliExampleGTF aspliFeaturesExample aspliJunctionDUexample aspliTargetsExample binbased binbased<-binGenome binsDU binsDU<-condition.order containsGenesAndBins containsJunctions countsb countsb<-countse1i countse1i<-countsg countsg<-countsie2 countsie2<-countsj countsj<-DUreport DUreport.norm DUreport.offset DUreportBinSplice esPSI esPSI<-exportIntegratedSignals exportSplicingReports featuresb featuresb<-featuresg featuresg<-featuresj featuresj<-filterDU filters filters<-filterSignals gbCounts gbDUreport genesDE genesDE<-getConditions integrateSignals irPIR irPIR<-jalt jalt<-jCounts jDUreport jes jes<-jir jir<-joint joint<-junctionDUreport junctionsDU junctionsDU<-junctionsPIR junctionsPIR<-junctionsPJU junctionsPJU<-loadBAM localebased localebased<-localec localec<-localej localej<-mergeBinDUAS plotBins plotGenomicRegions rds rdsb rdsb<-rdsg rdsg<-readCounts show signals signals<-splicingReport subset subsetBams subsetTargets targets transcriptExons transcriptExons<-writeAll writeAS writeCounts writeDU writeJDU writeRds writeSplicingReport

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocStyle biomaRt Biostrings biovizBase bit bit64 bitops blob bookdown BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr DT edgeR ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl otel pbmcapply pillar pkgconfig plyr png prettyunits progress promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils UpSetR utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

ASpli

Rendered fromASpli.Rnwusingutils::Sweave

Last update: 2024-03-20
Started: 2023-09-05

Citation

Development and contributors

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