curatedOvarianData

This is the development version of curatedOvarianData; for the stable release version, see curatedOvarianData.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

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] ORCID: 0000-0003-2725-0694 , NCI [fnd] (GrantNo.: U24CA289073)

Maintainer: Levi Waldron <lwaldron.research at gmail.com>

Citation (from within R, enter citation("curatedOvarianData")):

Benjamin Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron. curatedOvarianData: Clinically Annotated Data for the Ovarian Cancer Transcriptome. doi:10.18129/B9.bioc.curatedOvarianData, R package version 1.51.5, https://bioconductor.org/packages/curatedOvarianData.

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")

## 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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ArrayExpress, CancerData, ExperimentData, ExpressionData, GEO, MicroarrayData, OvarianCancerData, RNASeqData, miRNAData
Version	1.51.5
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
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

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, r-universe

Package Archives

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

Source Package	curatedOvarianData_1.51.5.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