Package: OSTA 1.3.1

Lukas M. Weber

OSTA: Orchestrating Spatial Transcriptomics Analysis with Bioconductor

This package contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" online book. This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial transcriptomics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets.

Authors:Helena L. Crowell [aut], Mark D. Robinson [aut], Stephanie C. Hicks [aut], Lukas M. Weber [aut, cre]

OSTA_1.3.1.tar.gz
OSTA_1.3.1.tgz(r-4.6-any)OSTA_1.3.1.tgz(r-4.5-any)
OSTA_1.3.1.tar.gz(r-4.7-any)OSTA_1.3.1.tar.gz(r-4.6-any)
OSTA_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OSTA/json (API)

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

Bug tracker:https://github.com/lmweber/osta/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

spatialsinglecellgeneexpressiontranscriptomicsanalysis-workflowsbioconductorspatial-transcriptomicsspatially-resolved-transcriptomicsopenjdk

6.27 score 114 stars 0 exports 467 dependencies

Last updated from:ca9ebaa54a. Checks:3 WARNING, 1 ERROR, 5 FAIL, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING543
linux-develWARNING528
source / vignettesERROR649
linux-releaseWARNING393
macos-releaseFAIL172
macos-oldrelFAIL190
windows-develFAIL404
windows-releaseFAIL405
windows-oldrelFAIL427
wasm-releaseOK524

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seanndataRannotateAnnotationDbiAnnotationFilterAnnotationHubaricodearrowashaskpassassertthatassortheadattemptAUCellbabelgenebackportsBanksybase64encbasiliskBayesSpacebdsmatrixbeachmatbeeswarmbenchmarkmebenchmarkmeDataBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64bitopsblobblusterbootBRISCbroombslibcachemcarcarDataCARDspacheckmatecigarillocirclizeclassClassifyRclassIntclicliprclueclustercodacodetoolscolorspacecommonmarkComplexHeatmapconcavemanconfigcorrplotcowplotcoxmecpp11crayoncrosstalkcrulcurlcytomapperdata.tableDBIdbplyrdbscandcanrDelayedArrayDelayedMatrixStatsdeldirDEoptimRDerivdeSolveDESpacedichromatdigestdir.expiryDirichletRegdistancesdoBydoMCdoParalleldoRNGdotCall64dplyrdqrngDropletUtilsDTe1071EBImageedgeRensembldbescheRevaluateExperimentHubfarverfastmapfastmatrixfdafdsfftwtoolsfieldsfilelockFNNfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgamm4genefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgeometriesGetoptLongggbeeswarmggcorrplotggforceggfortifyggfunggh4xggnewscaleggplot2ggpubrggraphggrepelggsciggsideggsignifggspavisggthemesggupsetglmnetGlobalOptionsgluegoftestgolemgraphgraphlayoutsgridBasegridExtragrpregGSEABasegtablegtoolsgypsumh5mreadharmonyHDF5ArrayhdrcdeherehexbinhexDensityhighrhmshoodscanRhtmltoolshtmlwidgetshttpcodehttpuvhttrhttr2igraphimcdatasetsimcRtoolsinsightIRangesirlbaisobanditeratorsjanitorjpegjquerylibjsonlitejsonvalidateKEGGRESTkernlabKernSmoothknitrkslabelinglambda.rlaterlatticelazyevalLearnBayesleidenAlglifecyclelimmalme4lmerTestlmtestlocfitlubridatelwgeommagicmagickmagrittrmapprojmapsmarginaleffectsMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxLikmclustmcmcMCMCpackmemoisememusemetapodmgcvmicrobenchmarkmimeminqamiscToolsmixtoolsmodelrmsigdbrmultcompMultiAssayExperimentmulticoolmuSpaDatamvtnormnlmenloptrNMFnnetnnlsnnSVGnumDerivopensslopenxlsxosfrOSTA.dataotelpaletteerpalspatchworkpbapplypbkrtestpbmcapplypbspcaPPpheatmappillarpkgconfigplotlyplyrpngpolyclippolynompracmaprettyunitsprismaticpROCprogresspromisesProtGenericsproxypurrrquadprogquantregR.methodsS3R.ooR.utilsR6rainbowrangerRANNrappdirsrasterrbibutilsRBioFormatsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppHungarianRcppMLRcppProgressRcppTOMLRCurlrdistRdpackreadrreformulasrefundregistryrematch2reshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibRigraphlibrJavarjsonrlangRLRsimrmarkdownrngtoolsrobustbaserpartrprojrootRsamtoolsRSpectraRSQLiterstatixrstudioapirsvdrtracklayerRTriangleRtsnes2S4ArraysS4VectorsS7sandwichsassScaledMatrixscalesscamscaterscatterpiesccorescicosciderscranscrapperscRNAseqscuttlesegmentedSeqinfosessioninfosfSFEDatasfheadersshapeshinyshinydashboardshinyWidgetssimpleSegSingleCellExperimentSingleRsitmosmoothrsnakecasesnowsostasourcetoolsspSpaceTrooperspacexrspamSparseArraySparseMsparseMatrixStatsSpatialExperimentSpatialExperimentIOspatialFDASpatialFeatureExperimentspatialLIBDSpatialPackspatialregspatstatspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsspDataspdepspicyRSpotSweeperstatmodSTexampleDatastringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorTENxIOterratextshapingTH.datatibbletidygraphtidyrtidyselecttifftimechangetimeDatetinytextriebeardtweenrtzdbUCSC.utilsunitsurcaurltoolsutf8uwotV8vctrsviporviridisviridisLiteVisiumIOVoyagervroomwithrwkwrMiscxfunxgboostXMLxtableXVectoryamlyulab.utilszeallotzipzoo