imageTCGAutils

Utility functions for working with histopathology images

Bioconductor version: 3.23 · Package version: 1.0.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("imageTCGAutils")

Details

Maintainer	Ilaria Billato <ilaria.billato@phd.unipd.it>
Author	Marcel Ramos [aut] (ORCID: <https://orcid.org/0000-0002-3242-0582>, affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA), Ilaria Billato [aut, cre] (ORCID: <https://orcid.org/0000-0002-3335-3254>, affiliation: Department of Biology, University of Padova), Eslam Abousamra [ctb] (affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA)
License	Artistic-2.0
URL	https://github.com/waldronlab/imageTCGAutils
Bug Reports	https://github.com/waldronlab/imageTCGAutils/issues
Downloads rank	52
Source branch	RELEASE_3_23
biocViews	Preprocessing, Software, WorkflowStep

Documentation

imageTCGAutils

Download

Source package

Dependencies

Depends: R (>= 4.5.0)

Imports: BiocBaseUtils, data.table, dplyr, grDevices, methods, rlang, S4Vectors, SpatialExperiment, SummarizedExperiment

Suggests: anndataR, BiocStyle, imageFeatureTCGA, ggplot2, knitr, paws, rhdf5, rmarkdown, sfdep, spdep, SpatialFeatureExperiment, tinytest

Reverse dependencies

Suggests Me (1): imageFeatureTCGA