imageFeatureTCGA
Import features from hovernet, provgigapath into a MultiAssayExperiment
Bioconductor version: 3.24 · Package version: 1.1.6
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("imageFeatureTCGA")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 [aut] (affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA), Sehyun Oh [aut] (ORCID: <https://orcid.org/0000-0002-9490-3061>, affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA) |
| License | Artistic-2.0 |
| URL | https://github.com/waldronlab/imageFeatureTCGA |
| Bug Reports | https://github.com/waldronlab/imageFeatureTCGA/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/imageFeatureTCGA/ |
Citation
From within R, enter citation("imageFeatureTCGA"):
Marcel Ramos, Ilaria Billato, Eslam Abousamra, Sehyun Oh. imageFeatureTCGA: Import features from hovernet, provgigapath into a MultiAssayExperiment. doi:10.18129/B9.bioc.imageFeatureTCGA, R package version 1.1.6, https://bioconductor.org/packages/imageFeatureTCGA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | imageFeatureTCGA_1.1.6.tar.gz |
| Windows binary (x86_64) | imageFeatureTCGA_1.1.6.zip |
| macOS binary (arm64) | imageFeatureTCGA_1.1.6.tgz |
| macOS binary (x86_64) | imageFeatureTCGA_1.1.6.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocBaseUtils, BiocFileCache, BiocIO, BumpyMatrix, dplyr, httr2, IRanges, methods, readr, rjsoncons, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, TCGAutils, TENxIO, tibble, utils
Suggests: AnnotationDbi, anndataR, arrow, BiocStyle, BiocParallel, cowplot, curatedTCGAData, curl, ggplot2, imageTCGAutils, knitr, png, RColorBrewer, rhdf5, rmarkdown, SpatialFeatureExperiment, tinytest, yaml