curatedOvarianData
This is the development version of curatedOvarianData; for the stable release version, see curatedOvarianData.
Clinically Annotated Data for the Ovarian Cancer Transcriptome
Bioconductor version: Development (3.24)
Manually curated human ovarian cancer ExpressionSet objects from 30 studies, with uniformly processed expression data and standardized clinical metadata including survival outcomes. Datasets are hosted on Zenodo and downloaded on first use, then cached locally with BiocFileCache. Includes a configurable script for rule-based creation of filtered dataset lists for meta-analysis.
Author: Benjamin Ganzfried [aut], Markus Riester [aut], Steve Skates [aut], Victoria Wang [aut], Thomas Risch [aut], Benjamin Haibe-Kains [aut], Svitlana Tyekucheva [aut], Jie Ding [aut], Ina Jazic [aut], Michael Birrer [aut], Giovanni Parmigiani [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre]
, NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Levi Waldron <lwaldron.research at gmail.com>
citation("curatedOvarianData")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("curatedOvarianData")
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("curatedOvarianData")| curatedOvarianData | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ArrayExpress, CancerData, ExperimentData, ExpressionData, GEO, MicroarrayData, OvarianCancerData, RNASeqData, miRNAData |
| Version | 1.51.4 |
| License | Artistic-2.0 |
| Depends | Biobase, R (>= 4.6.0) |
| Imports | BiocFileCache, tools, utils |
| System Requirements | |
| URL | https://github.com/waldronlab/curatedOvarianData |
| Bug Reports | https://github.com/waldronlab/curatedOvarianData/issues |
See More
| Suggests | BiocStyle, futile.logger, genefilter, knitr, logging, metafor, rmarkdown, testthat (>= 3.0.0), survival, sva, xtable |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | doppelgangR, TOP |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | curatedOvarianData_1.51.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/curatedOvarianData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/curatedOvarianData |
| Package Short Url | https://bioconductor.org/packages/curatedOvarianData/ |
| Package Downloads Report | Download Stats |