curatedCRCData

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

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

Colorectal Cancer Gene Expression Analysis

Bioconductor version: Development (3.24)

Manually curated human colorectal cancer ExpressionSet objects from 34 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: Princy Parsana [aut], Markus Riester [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre] ORCID: 0000-0003-2725-0694 , National Cancer Institute [fnd] (5U24CA180996)

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

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

Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron. curatedCRCData: Colorectal Cancer Gene Expression Analysis. doi:10.18129/B9.bioc.curatedCRCData, R package version 2.45.6, https://bioconductor.org/packages/curatedCRCData.

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("curatedCRCData")

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("curatedCRCData")

curatedCRCData	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CancerData, ColonCancerData, ExperimentData, ExpressionData, GEO, MicroarrayData, RNASeqData
Version	2.45.6
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	Artistic-2.0
Depends	R (>= 4.6.0), Biobase
Imports	BiocFileCache, tools, utils
System Requirements
URL	https://github.com/waldronlab/curatedCRCData
Bug Reports	https://github.com/waldronlab/curatedCRCData/issues

Suggests	survival, testthat (>= 3.0.0), metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	curatedCRCData_2.45.6.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/curatedCRCData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/curatedCRCData
Package Short Url	https://bioconductor.org/packages/curatedCRCData/
Package Downloads Report	Download Stats