imageTCGAutils
This is the development version of imageTCGAutils; to use it, please install the devel version of Bioconductor.
Utility functions for working with histopathology images
Bioconductor version: Development (3.23)
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.
Author: Marcel Ramos [aut] (ORCID:
, affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA), Ilaria Billato [aut, cre] (ORCID:
, affiliation: Department of Biology, University of Padova), Eslam Abousamra [ctb] (affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA)
Maintainer: Ilaria Billato <ilaria.billato at phd.unipd.it>
citation("imageTCGAutils")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("imageTCGAutils")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("imageTCGAutils")| imageTCGAutils | HTML | R Script |
| Reference Manual |
Details
| biocViews | Preprocessing, Software, WorkflowStep |
| Version | 0.99.24 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | BiocBaseUtils, data.table, dplyr, grDevices, methods, rlang, S4Vectors, SpatialExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/waldronlab/imageTCGAutils |
| Bug Reports | https://github.com/waldronlab/imageTCGAutils/issues |
See More
| Suggests | anndataR, BiocStyle, imageFeatureTCGA, ggplot2, knitr, paws, rhdf5, rmarkdown, sfdep, spdep, SpatialFeatureExperiment, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | imageTCGAutils_0.99.24.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | imageTCGAutils_0.99.24.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/imageTCGAutils |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/imageTCGAutils |
| Bioc Package Browser | https://code.bioconductor.org/browse/imageTCGAutils/ |
| Package Short Url | https://bioconductor.org/packages/imageTCGAutils/ |
| Package Downloads Report | Download Stats |