Package: OSCA.basic 1.21.0

Peter Hickey

OSCA.basic: Single-Cell Analysis Basics

Deploys basic analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the steps of a simple single-cell RNA-seq analysis, involving quality control, normalization, various forms of dimensionality reduction, clustering into subpopulations, detection of marker genes, and annotation of cell types. It is intended for users who already have some familiarity with R and want to get hands-on with some basic single-cell analyses.

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

OSCA.basic_1.21.0.tar.gz
OSCA.basic_1.21.0.zip(r-4.7)OSCA.basic_1.21.0.zip(r-4.6)OSCA.basic_1.21.0.zip(r-4.5)
OSCA.basic_1.21.0.tgz(r-4.6-any)OSCA.basic_1.21.0.tgz(r-4.5-any)
OSCA.basic_1.21.0.tar.gz(r-4.7-any)OSCA.basic_1.21.0.tar.gz(r-4.6-any)
OSCA.basic_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OSCA.basic/json (API)

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

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

On CRAN:

Conda:

immunooncologyworkflowworkflowsinglecellworkflow

5.26 score 15 stars 0 exports 245 dependencies

Last updated from:4653f341a2. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE599
linux-devel-x86_64WARNING665
source / vignettesOK1806
linux-release-x86_64WARNING671
macos-release-arm64WARNING289
macos-oldrel-arm64WARNING386
windows-develWARNING666
windows-releaseWARNING629
windows-oldrelWARNING638
wasm-releaseOK609

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seannotateAnnotationDbiAnnotationFilterAnnotationHubapclusteraskpassassertthatassortheadAUCellbase64encbatchelorbeachmatbeeswarmbenchmarkmebenchmarkmeDataBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStyleBiocVersionBiostringsbitbit64bitopsblobblusterbookdownbslibcachemCairocelldexcigarillocliclusterClusterRCodeDependscodetoolscoopcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdendextendDEoptimRdigestdir.expirydoParalleldplyrdqrngDropletTestFilesDropletUtilsdynamicTreeCutedgeRelasticnetEnsDb.Hsapiens.v86ensembldbevaluateExperimentHubfarverfastmapfilelockFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggplot2ggrastrggrepelglobalsgluegmpGO.dbgraphgridExtraGSEABasegtablegypsumh5mreadHCADataHDF5Arrayhighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesirlbaisobanditeratorsjquerylibjsonlitejsonvalidateKEGGRESTkernlabknitrlabelinglambda.rlarslaterlatticelazyevallifecyclelimmalistenvlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmbkmeansmemoisemetapodmimemixtoolsnlmeopensslorg.Hs.eg.dborg.Mm.eg.dborigamiOSCA.workflowsotelparallellypheatmappillarpkgconfigplotlypngpromisesProtGenericspurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRCurlRdpackrebookResidualMatrixrestfulrrhdf5rhdf5filtersRhdf5libRhtslibRigraphlibrjsonrlangrmarkdownRMTstatrobustbaseRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscPCAscranscrapperscRNAseqscuttlesegmentedSeqinfoSingleCellExperimentSingleRsitmosnowSparseArraysparseMatrixStatssparsepcastatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotV8vctrsviporviridisviridisLitewithrxfunXMLxtableXVectoryaml

Link to book

Rendered fromstub.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2021-01-18
Started: 2021-01-18