Package: OSCA.advanced 1.21.0

Ludwig Geistlinger

OSCA.advanced: Advanced Single-Cell Analysis

Deploys the advanced analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the more complex steps of a single-cell RNA-seq analysis ranging from doublet detection, cell cycle assignment, specific steps for processing droplet data, nuclei-specific analyses, trajectory analyses, integrated analyses with protein abundances, and interactive visualization. It also elaborates on some of the basic analysis steps, focusing on alternative strategies and theoretical considerations. It is intended for readers who are already familiar with basic single-cell analyses, possibly after reading some of the prior books in this collection.

Authors:Robert Amezquita [aut], Aaron Lun [aut], Stephanie Hicks [aut], Raphael Gottardo [aut], Ludwig Geistlinger [cre], Peter Hickey [ctb]

OSCA.advanced_1.21.0.tar.gz
OSCA.advanced_1.21.0.zip(r-4.7)OSCA.advanced_1.21.0.zip(r-4.6)OSCA.advanced_1.21.0.zip(r-4.5)
OSCA.advanced_1.21.0.tgz(r-4.6-any)OSCA.advanced_1.21.0.tgz(r-4.5-any)
OSCA.advanced_1.21.0.tar.gz(r-4.7-any)OSCA.advanced_1.21.0.tar.gz(r-4.6-any)
OSCA.advanced_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OSCA.advanced/json (API)

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

Bug tracker:https://github.com/osca-source/osca.advanced/issues

On CRAN:

Conda:

immunooncologyworkflowworkflowsinglecellworkflow

4.47 score 14 stars 0 exports 321 dependencies

Last updated from:84c44efb72. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE544
linux-devel-x86_64WARNING917
source / vignettesERROR2254
linux-release-x86_64WARNING655
macos-release-arm64WARNING389
macos-oldrel-arm64WARNING405
windows-develWARNING714
windows-releaseWARNING637
windows-oldrelWARNING739
wasm-releaseOK499

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seannotateAnnotationDbiAnnotationFilterAnnotationHubapclusteraskpassassertthatassortheadAUCellbabelgenebackportsbase64encbasiliskbatchelorbeachmatbeeswarmbenchmarkmebenchmarkmeDataBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStyleBiocVersionBiostringsbitbit64bitopsblobblusterbookdownbslibBumpyMatrixcachemCairocaToolscelldexcheckmatecigarillocirclizecliclueclusterClusterRclustreeCodeDependscodetoolscolorspacecolourpickercombinatcommonmarkComplexHeatmapcoopcorralcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdendextenddensvisDEoptimRdichromatdigestdir.expirydoParalleldplyrdqrngDropletTestFilesDropletUtilsDTdynamicTreeCutedgeRelasticnetEnsDb.Hsapiens.v86ensembldbevaluateExperimentHubfarverfastICAfastmapfilelockFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggbeeswarmggforceggplot2ggraphggrastrggrepelggthemesGlobalOptionsglobalsgluegmpGO.dbgplotsgraphgraphlayoutsgridExtraGSEABasegtablegtoolsgypsumh5mreadHCADataHDF5Arrayherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesirlbaiSEEisobanditeratorsjquerylibjsonlitejsonvalidateKEGGRESTkernlabKernSmoothknitrlabelinglambda.rlarslaterlatticelazyevallifecyclelimmalistenvlistviewerlocfitmagickmagrittrmapprojmapsMASSMatrixMatrixGenericsmatrixStatsmbkmeansmclustmemoisemetapodmgcvmimeminiUImixtoolsMouseGastrulationDatamsigdbrMultiAssayExperimentmumosanlmeopensslorg.Hs.eg.dborg.Mm.eg.dborigamiOSCA.basicOSCA.multisampleOSCA.workflowsotelpalsparallellypbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprincurvepromisesProtGenericspurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRcppTOMLRCurlRdpackrebookreshape2ResidualMatrixrestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibRigraphlibrintrojsrjsonrlangrmarkdownRMTstatrobustbaserprojrootRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscDblFinderscPCAscranscrapperscRNAseqscuttlesegmentedSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentSingleRsitmoslingshotsniftersnowsourcetoolsSparseArraysparseMatrixStatssparsepcaSpatialExperimentstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsTENxBrainDataTENxPBMCDatatextshapingtibbletidygraphtidyrtidyselecttinytextradeSeqTrajectoryUtilstransportTSCANtweenrUCSC.utilsutf8uwotV8vctrsvelociraptorviporviridisviridisLitewithrxfunxgboostXMLxtableXVectoryamlzellkonverter