FieldEffectCrc

DOI: 10.18129/B9.bioc.FieldEffectCrc    

Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

Bioconductor version: Release (3.14)

Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

Author: Christopher Dampier [aut, cre] , Bioconductor Package Maintainer [ctb]

Maintainer: Christopher Dampier <chd5n at virginia.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("FieldEffectCrc")

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("FieldEffectCrc")

 

HTML	R Script	SummarizedExperiments of colorectal transcriptomes
PDF		Reference Manual
Text		NEWS

Details

biocViews	ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, ReproducibleResearch, SequencingData, Tissue
Version	1.4.0
License	Artistic-2.0
Depends	utils
Imports	BiocStyle, RUnit, SummarizedExperiment, ExperimentHub(>= 0.99.6), AnnotationHub, DESeq2
LinkingTo
Suggests	knitr, rmarkdown, BiocGenerics, sva, BiocManager
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html
BugReports	https://github.com/Bioconductor/FieldEffectCrc/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FieldEffectCrc_1.4.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/FieldEffectCrc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FieldEffectCrc
Package Short Url	https://bioconductor.org/packages/FieldEffectCrc/
Package Downloads Report	Download Stats