Package: imageFeatureTCGA 1.0.0

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:Marcel Ramos [aut], Ilaria Billato [aut, cre], Eslam Abousamra [aut], Sehyun Oh [aut]

imageFeatureTCGA_1.0.0.tar.gz
imageFeatureTCGA_1.0.0.zip(r-4.7)imageFeatureTCGA_1.0.0.zip(r-4.6)imageFeatureTCGA_1.0.0.zip(r-4.5)
imageFeatureTCGA_1.0.0.tgz(r-4.6-any)imageFeatureTCGA_1.0.0.tgz(r-4.5-any)
imageFeatureTCGA_1.0.0.tar.gz(r-4.7-any)imageFeatureTCGA_1.0.0.tar.gz(r-4.6-any)
imageFeatureTCGA_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
imageFeatureTCGA/json (API)
NEWS

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

Bug tracker:https://github.com/waldronlab/imagefeaturetcga/issues

On BioConductor:imageFeatureTCGA-1.1.0(bioc 3.24)imageFeatureTCGA-1.0.0(bioc 3.23)

softwareinfrastructuredataimportdatarepresentation

6.00 score 1 stars 1 packages 89 downloads 10 exports 116 dependencies

Last updated from:39ba8ff843 (on RELEASE_3_23). Checks:1 NOTE, 6 OK, 3 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE248
linux-devel-x86_64OK490
source / vignettesOK383
linux-release-x86_64OK512
macos-release-arm64OK315
macos-oldrel-arm64OK461
windows-develERROR306
windows-releaseERROR311
windows-oldrelERROR341
wasm-releaseOK213

Exports:embeddingStackgetCataloggetFileURLsHoverNetimportlinkTCGApathProvGigaProvGigaListshow

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobBumpyMatrixcachemcigarilloclicliprcodetoolscpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesglueh5mreadHDF5Arrayhmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6RaggedExperimentrappdirsRcppRCurlreadrrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrjsonconsrlangRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsselectrSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsysTCGAutilsTENxIOtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVectoryaml

Import HoverNet and ProvGigaPath features with imageFeatureTCGA

Ilaria Billato

Rendered fromimageFeatureTCGA.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-03-02
Started: 2026-02-10

Readme and manuals

Help Manual

Help pageTopics
Create an embedding stack from a ProvGigaList objectembeddingStack
Download the catalog of available HoVerNet and ProvGigaPath filesgetCatalog getFileURLs
Import Hovernet JSON, H5AD, and PNG files into Bioconductor classes.HoverNetPNG HoverNet HoverNet-class HoverNetH5AD-class HoverNetJSON-class HoverNetPNG-class import,HoverNetH5AD,ANY,ANY-method import,HoverNetJSON,ANY,ANY-method import,HoverNetPNG,ANY,ANY-method show,HoverNetJSON-method
Link MultiAssayExperiment object to TCGA datalinkTCGA
Import ProvGiga slide-level data into a Bioconductor class objectimport,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