imageFeatureTCGA
This is the development version of imageFeatureTCGA; to use it, please install the devel version of Bioconductor.
Import features from hovernet, provgigapath into a MultiAssayExperiment
Bioconductor version: Development (3.23)
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.
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 [aut] (affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA), Sehyun Oh [aut] (ORCID:
, affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA)
Maintainer: Ilaria Billato <ilaria.billato at phd.unipd.it>
citation("imageFeatureTCGA")):
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("imageFeatureTCGA")
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("imageFeatureTCGA")| imageFeatureTCGA | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 0.99.69 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | BiocBaseUtils, BiocFileCache, BiocIO, BumpyMatrix, dplyr, httr2, IRanges, methods, readr, rjsoncons, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, TCGAutils, TENxIO, tibble, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/imageFeatureTCGA |
| Bug Reports | https://github.com/waldronlab/imageFeatureTCGA/issues |
See More
| Suggests | AnnotationDbi, anndataR, BiocStyle, BiocParallel, cowplot, curatedTCGAData, curl, ggplot2, imageTCGAutils, knitr, png, RColorBrewer, rhdf5, rmarkdown, SpatialFeatureExperiment, tinytest, yaml |
| 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 | imageFeatureTCGA_0.99.69.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | imageFeatureTCGA_0.99.69.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/imageFeatureTCGA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/imageFeatureTCGA |
| Bioc Package Browser | https://code.bioconductor.org/browse/imageFeatureTCGA/ |
| Package Short Url | https://bioconductor.org/packages/imageFeatureTCGA/ |
| Package Downloads Report | Download Stats |