Package: OSCA.multisample 1.21.0

Alan OCallaghan

OSCA.multisample: OSCA for Multiple Samples

Deploys the multi-sample analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book. This describes the handling of multiple samples in a single-cell RNA-seq analysis, starting with integration of multiple datasets into a common space for consistent analyses, differential expression comparisons between conditions based on pseudo-bulk samples, and differential abundance analyses for cell subpopulations. 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], Alan O'Callaghan [cre]

OSCA.multisample_1.21.0.tar.gz
OSCA.multisample_1.21.0.zip(r-4.7)OSCA.multisample_1.21.0.zip(r-4.6)OSCA.multisample_1.21.0.zip(r-4.5)
OSCA.multisample_1.21.0.tgz(r-4.6-any)OSCA.multisample_1.21.0.tgz(r-4.5-any)
OSCA.multisample_1.21.0.tar.gz(r-4.7-any)OSCA.multisample_1.21.0.tar.gz(r-4.6-any)
OSCA.multisample_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OSCA.multisample/json (API)

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

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

On CRAN:

Conda:

immunooncologyworkflowworkflowsinglecellworkflow

3.56 score 6 stars 0 exports 238 dependencies

Last updated from:b71a42db9d. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE495
linux-devel-x86_64WARNING559
source / vignettesERROR589
linux-release-x86_64WARNING564
macos-release-arm64WARNING325
macos-oldrel-arm64WARNING338
windows-develWARNING1225
windows-releaseWARNING1076
windows-oldrelWARNING1078
wasm-releaseOK445

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seAnnotationDbiAnnotationFilterAnnotationHubaskpassassertthatassortheadbase64encbatchelorbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStyleBiocVersionBiostringsbitbit64bitopsblobblusterbookdownbslibBumpyMatrixcachemCairocaToolscelldexcigarillocliclusterCodeDependscodetoolscombinatcommonmarkcoopcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydplyrdqrngDropletTestFilesDropletUtilsdynamicTreeCutedgeRelasticnetEnsDb.Hsapiens.v86ensembldbevaluateExperimentHubfarverfastICAfastmapfilelockFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggplot2ggrastrggrepelglobalsgluegplotsgraphgridExtragtablegtoolsgypsumh5mreadHCADataHDF5Arrayhighrhtmltoolshttpuvhttrhttr2igraphIRangesirlbaisobandjquerylibjsonlitejsonvalidateKEGGRESTkernlabKernSmoothknitrlabelinglambda.rlarslaterlatticelazyevallifecyclelimmalistenvlocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmclustmemoisemetapodmgcvmimeMouseGastrulationDatanlmeopensslorg.Hs.eg.dborg.Mm.eg.dborigamiOSCA.workflowsotelparallellypheatmappillarpkgconfigplyrpngpromisesProtGenericspurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlRdpackrebookResidualMatrixrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscPCAscranscRNAseqscuttleSeqinfoshinySingleCellExperimentSingleRsitmosnowsourcetoolsSparseArraysparseMatrixStatssparsepcaSpatialExperimentstatmodstringistringrSummarizedExperimentsyssystemfontsTENxPBMCDatatextshapingtibbletidyrtidyselecttinytexTrajectoryUtilsTSCANUCSC.utilsutf8uwotV8vctrsviporviridisviridisLitewithrxfunXMLxtableXVectoryaml