Package: saseR 1.1.0
Alexandre Segers
saseR: Scalable Aberrant Splicing and Expression Retrieval
saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{https://doi.org/10.1101/2023.06.29.547014}.
Authors:
saseR_1.1.0.tar.gz
saseR_1.1.0.zip(r-4.5)saseR_1.1.0.zip(r-4.4)saseR_1.1.0.zip(r-4.3)
saseR_1.1.0.tgz(r-4.4-any)saseR_1.1.0.tgz(r-4.3-any)
saseR_1.1.0.tar.gz(r-4.5-noble)saseR_1.1.0.tar.gz(r-4.4-noble)
saseR_1.1.0.tgz(r-4.4-emscripten)saseR_1.1.0.tgz(r-4.3-emscripten)
saseR.pdf |saseR.html✨
saseR/json (API)
NEWS
| # Install 'saseR' in R: |
| install.packages('saseR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/statomics/saser/issues
- ASpliSE - ASpliSE
- SEbins - SEbins
- SEgenes - SEgenes
- SEjunctions - SEjunctions
- features - Features
On BioConductor:saseR-1.1.0(bioc 3.20)saseR-1.0.0(bioc 3.19)
Last updated 2 months agofrom:a1754de138
Exports:BamtoAspliCountscalculateOffsetsconvertASplisaseRfindEncodingDimsaseRfit
Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassASpliassertthatbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocStylebiomaRtBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDEoptimRDESeq2DEXSeqdichromatdigestdplyrDTedgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2hwriterigraphinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetopensslpbmcapplypcaPPpillarpkgconfigplogrplyrpngpracmaprecrecprettyunitsprogresspromisesProtGenericsPRROCpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrobustbaserpartrrcovRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsUpSetRutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ASpliSE | ASpliSE |
| Converting BAM files to an ASpli-SummarizedExperiment, which contains gene, bin and junction counts. | BamtoAspliCounts |
| calculating the offsets to perform aberrant expression or splicing analysis. | calculateOffsets |
| Converting SummarizedExperiment with different ASpli-counts to gene, bin or junction level counts. | convertASpli |
| features | features |
| saseRExample | saseRExample |
| Determine the optimal number of latent factors to detect outlier gene expression or splicing | saseRfindEncodingDim |
| Searching for aberrant expression or splicing. | saseRfit |
| SEbins | SEbins |
| SEgenes | SEgenes |
| SEjunctions | SEjunctions |