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FieldEffectCrc

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
SummarizedExperiments of colorectal transcriptomes HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, ReproducibleResearch, SequencingData, Tissue
Version 1.12.0
License Artistic-2.0
Depends utils
Imports BiocStyle, RUnit, SummarizedExperiment, ExperimentHub(>= 0.99.6), AnnotationHub, DESeq2
System Requirements
URL http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html
Bug Reports https://github.com/Bioconductor/FieldEffectCrc/
See More
Suggests knitr, rmarkdown, BiocGenerics, sva, BiocManager
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Package Archives

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

Source Package FieldEffectCrc_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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