imageFeatureTCGA
This is the released version of imageFeatureTCGA; for the devel version, see imageFeatureTCGA.
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:
, 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
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 | HistoImagePlot |
| Suggests Me | imageTCGAutils |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/imageFeatureTCGA/ |
| Package Short Url | https://bioconductor.org/packages/imageFeatureTCGA/ |
| Package Downloads Report | Download Stats |