Introduction | Installation | Loading packages | Import Prov-GigaPath tile level embeddings | Embedding PCA | Spatial Patterns | Adding HoverNet Nuclei Features | Visualizing Hovernet nuclei vs tile coordinates to see that they do not match | Scale factor between nuclei coordinates and tile coordinates | Session Info | References
Package: imageTCGAutils 1.1.5
Ilaria Billato
imageTCGAutils: Utility functions for working with histopathology images
Utility functions for working with CONCH data, listing remote files. One function assigns HoverNet nuclei to ProvGigaPath tiles with a scale factor to align coordinates. Provides internal utility functions for 'imageFeatureTCGA' and most functions are not meant for end users.
Authors:
imageTCGAutils_1.1.5.tar.gz
imageTCGAutils_1.1.5.zip(r-4.7)imageTCGAutils_1.1.5.zip(r-4.6)imageTCGAutils_1.1.5.zip(r-4.5)
imageTCGAutils_1.1.5.tgz(r-4.6-any)imageTCGAutils_1.1.5.tgz(r-4.5-any)
imageTCGAutils_1.1.5.tar.gz(r-4.7-any)imageTCGAutils_1.1.5.tar.gz(r-4.6-any)
imageTCGAutils_1.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
imageTCGAutils/json (API)
| # Install 'imageTCGAutils' in R: |
| install.packages('imageTCGAutils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/imagetcgautils/issues
On BioConductor:imageTCGAutils-1.1.4(bioc 3.24)imageTCGAutils-1.0.0(bioc 3.23)
softwareworkflowsteppreprocessing
Last updated from:fbb892f622. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 239 | ||
| linux-devel-x86_64 | NOTE | 372 | ||
| source / vignettes | OK | 443 | ||
| linux-release-x86_64 | NOTE | 367 | ||
| macos-release-arm64 | NOTE | 289 | ||
| macos-oldrel-arm64 | NOTE | 221 | ||
| windows-devel | NOTE | 254 | ||
| windows-release | NOTE | 260 | ||
| windows-oldrel | NOTE | 253 | ||
| wasm-release | OK | 218 |
Exports:importCONCHlistHoverNetlistProvGigamatchHoverNetToTiles
Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curldata.tableDBIdbplyrDelayedArraydplyrfastmapfilelockgenericsGenomicRangesgluehttr2IRangeslatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Import CONCH as a SpatialFeatureExperiment | importCONCH |
| List available HoVerNet and Prov-Giga-Path data for TCGA cancers | listFiles listHoverNet listProvGiga |
| Match HoverNet Nuclei to ProvGigaPath Tiles | matchHoverNetToTiles |