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✨
card.svg |card.png
OSTA/json (API)
NEWS

# 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

6.35 score 113 stars 0 exports 471 dependencies

Last updated from:df45a78b77. Checks:1 FAILURE, 3 WARNING, 1 ERROR, 5 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksFAILURE478
linux-devel-x86_64WARNING617
source / vignettesERROR3650
linux-release-x86_64FAIL409
macos-release-arm64WARNING275
macos-oldrel-arm64WARNING253
windows-develFAIL506
windows-releaseFAIL517
windows-oldrelFAIL494
wasm-releaseFAIL492

Exports:

Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.seanndataRannotateAnnotationDbiAnnotationFilterAnnotationHubaricodearrowashaskpassassertthatassortheadattemptAUCellbabelgenebackportsBanksybase64encbasiliskBayesSpacebdsmatrixbeachmatbeeswarmbenchmarkmebenchmarkmeDataBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64bitopsblobblusterbootBRISCbroombslibcachemCairocarcarDataCARDspacheckmatecigarillocirclizeclassClassifyRclassIntclicliprclueclustercodacodetoolscolorspacecommonmarkComplexHeatmapconcavemanconfigcorrplotcowplotcoxmecpp11crayoncrosstalkcrulcurlcytomapperdata.tableDBIdbplyrdbscandcanrDelayedArrayDelayedMatrixStatsdeldirDEoptimRDerivdeSolveDESpacedichromatdigestdir.expiryDirichletRegdistancesdoBydoMCdoParalleldoRNGdotCall64dplyrdqrngDropletUtilsDTe1071EBImageedgeRensembldbescheRevaluateExperimentHubfarverfastmapfastmatrixfdafdsfftwtoolsfieldsfilelockFNNfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgamm4genefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgeometriesGetoptLongggbeeswarmggcorrplotggforceggfortifyggfunggh4xggnewscaleggplot2ggpubrggraphggrastrggrepelggsciggsideggsignifggspavisggthemesggupsetglmnetGlobalOptionsgluegoftestgolemgraphgraphlayoutsgridBasegridExtragrpregGSEABasegtablegtoolsgypsumh5mreadharmonyHDF5ArrayhdrcdeherehexbinhexDensityhighrhmshoodscanRhtmltoolshtmlwidgetshttpcodehttpuvhttrhttr2igraphimcdatasetsimcRtoolsinsightIRangesirlbaisobanditeratorsjanitorjpegjquerylibjsonlitejsonvalidateKEGGRESTkernlabKernSmoothknitrkslabelinglambda.rlaterlatticelazyevalLearnBayesleidenAlglifecyclelimmalme4lmerTestlmtestlocfitlubridatelwgeommagicmagickmagrittrmapprojmapsmarginaleffectsMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxLikmclustmcmcMCMCpackmemoisememusemetapodmgcvmicrobenchmarkmimeminqamiscToolsmixtoolsmodelrmsigdbrmultcompMultiAssayExperimentmulticoolmuSpaDatamvtnormnlmenloptrNMFnnetnnlsnnSVGnumDerivopensslopenxlsxosfrOSTA.dataotelpaletteerpalspatchworkpbapplypbkrtestpbmcapplypbspcaPPpheatmappillarpkgconfigplotlyplyrpngpolyclippolynompracmaprettyunitsprismaticpROCprogresspromisesProtGenericsproxypurrrquadprogquantregR.methodsS3R.ooR.utilsR6raggrainbowrangerRANNrappdirsrasterrbibutilsRBioFormatsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppDistRcppEigenRcppHungarianRcppMLRcppProgressRcppTOMLRCurlrdistRdpackreadrreformulasrefundregistryrematch2reshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibRigraphlibrJavarjsonrlangRLRsimrmarkdownrngtoolsrobustbaserpartrprojrootRsamtoolsRSpectraRSQLiterstatixrstudioapirsvdrtracklayerRTriangleRtsnes2S4ArraysS4VectorsS7sandwichsassScaledMatrixscalesscamscaterscatterpiesccorescicosciderscranscrapperscRNAseqscuttlesegmentedSeqinfosessioninfosfSFEDatasfheadersshapeshinyshinydashboardshinyWidgetssimpleSegSingleCellExperimentSingleRsitmosmoothrsnakecasesnowsostasourcetoolsspSpaceTrooperspacexrspamSparseArraySparseMsparseMatrixStatsspatialEcoSpatialExperimentSpatialExperimentIOspatialFDASpatialFeatureExperimentspatialLIBDSpatialPackspatialregspatstatspatstat.dataspatstat.explorespatstat.geomspatstat.linnetspatstat.modelspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsspDataspdepspicyRSpotSweeperstatmodSTexampleDatastringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorTENxIOterratextshapingTH.datatibbletidygraphtidyrtidyselecttifftimechangetimeDatetinytextriebeardtweenrtzdbUCSC.utilsunitsurcaurltoolsutf8uwotV8vctrsviporviridisviridisLiteVisiumIOVoyagervroomwithrwkwrMiscxfunxgboostXMLxtableXVectoryamlyulab.utilszeallotzipzoo