imageFeatureTCGA

This is the released version of imageFeatureTCGA; for the devel version, see imageFeatureTCGA.

All versions

3.24 (devel), 3.23 (release)

Import features from hovernet, provgigapath into a MultiAssayExperiment

Bioconductor version: Release (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: ORCID: 0000-0002-3242-0582 , affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA), Ilaria Billato [aut, cre] (ORCID: ORCID: 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: ORCID: 0000-0002-9490-3061 , affiliation: CUNY Graduate School of Public Health and Health Policy, New York, NY USA)

Maintainer: Ilaria Billato <ilaria.billato at phd.unipd.it>

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 1.0.0, https://bioconductor.org/packages/imageFeatureTCGA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Software
Version	1.0.0
In Bioconductor since	BioC 3.23 (R-4.6) (< 6 months)
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

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	HistoImagePlot
Suggests Me	imageTCGAutils
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	imageFeatureTCGA_1.0.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	imageFeatureTCGA_1.0.0.tgz
macOS Binary (sonoma-arm64)	imageFeatureTCGA_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/imageFeatureTCGA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/imageFeatureTCGA
Package Short Url	https://bioconductor.org/packages/imageFeatureTCGA/
Package Downloads Report	Download Stats