imageFeatureTCGA | Overview | Installation | Data structure and technical details | HoVerNet outputs | ProvGigaPath embeddings | Slide-level embeddings | Tile-level embeddings | Available Data | Formats | HoVerNet data | ProvGigaPath data | Importing HoVerNet data | Importing ProvGigaPath embeddings | Importing multiple ProvGigaPath files | Mixed level imports | See also | Shiny App: imageTCGA | Session Info
Package: imageFeatureTCGA 1.1.6
Ilaria Billato
imageFeatureTCGA: Import features from hovernet, provgigapath into a MultiAssayExperiment
The package imports data from HoverNet, and ProvGigaPath pipelines. Pipeline output data are hosted in a self-owned online repository. Package functionality conveniently incorporates pipeline data into existing MultiAssayExperiment instances from curatedTCGAData.
Authors:
imageFeatureTCGA_1.1.6.tar.gz
imageFeatureTCGA_1.1.6.zip(r-4.7)imageFeatureTCGA_1.1.6.zip(r-4.6)imageFeatureTCGA_1.1.6.zip(r-4.5)
imageFeatureTCGA_1.1.6.tgz(r-4.6-any)imageFeatureTCGA_1.1.6.tgz(r-4.5-any)
imageFeatureTCGA_1.1.6.tar.gz(r-4.7-any)imageFeatureTCGA_1.1.6.tar.gz(r-4.6-any)
imageFeatureTCGA_1.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
imageFeatureTCGA/json (API)
| # Install 'imageFeatureTCGA' in R: |
| install.packages('imageFeatureTCGA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/imagefeaturetcga/issues
On BioConductor:imageFeatureTCGA-1.1.5(bioc 3.24)imageFeatureTCGA-1.0.0(bioc 3.23)
softwareinfrastructuredataimportdatarepresentation
Last updated from:cce042259f. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 262 | ||
| linux-devel-x86_64 | OK | 540 | ||
| source / vignettes | OK | 427 | ||
| linux-release-x86_64 | OK | 420 | ||
| macos-release-arm64 | OK | 374 | ||
| macos-oldrel-arm64 | OK | 367 | ||
| windows-devel | OK | 413 | ||
| windows-release | OK | 436 | ||
| windows-oldrel | OK | 429 | ||
| wasm-release | OK | 244 |
Exports:embeddingStackgetCataloggetFileURLsHoverNetimportlinkTCGApathProvGigaProvGigaListshow
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobBumpyMatrixcachemcigarilloclicliprcodetoolscpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesglueh5mreadHDF5Arrayhmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6RaggedExperimentrappdirsRcppRCurlreadrrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrjsonconsrlangRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsselectrSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsysTCGAutilsTENxIOtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create an embedding stack from a ProvGigaList object | embeddingStack |
| Download the catalog of available HoVerNet and ProvGigaPath files | getCatalog getFileURLs |
| Import Hovernet JSON, H5AD, and PNG files into Bioconductor classes | .HoverNetPNG HoverNet HoverNet-class HoverNetH5AD-class HoverNetJSON-class HoverNetParquet-class HoverNetPNG-class import,HoverNetH5AD,ANY,ANY-method import,HoverNetJSON,ANY,ANY-method import,HoverNetParquet,ANY,ANY-method import,HoverNetPNG,ANY,ANY-method show,HoverNetJSON-method |
| Link MultiAssayExperiment object to TCGA data | linkTCGA |
| Import ProvGiga slide-level data into a Bioconductor class object | import,ProvGigaCSV,ANY,ANY-method ProvGiga ProvGiga-class ProvGigaCSV-class show,ProvGiga-method |
| ProvGigaList class for handling lists of ProvGiga objects | .ProvGigaList import,ProvGigaList,ANY,ANY-method path,ProvGigaList-method ProvGigaList ProvGigaList-class |