FieldEffectCrc

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see FieldEffectCrc.

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

Bioconductor version: 3.17

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ColonCancerData, ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, ReproducibleResearch, SequencingData, Tissue

Version 1.10.0

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/

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_1.10.0.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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