DGEobj: Differential Gene Expression (DGE) Analysis Results Data Object

Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows – it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).

Version:	1.1.2
Depends:	R (≥ 3.5.0)
Imports:	assertthat, magrittr, stringr, utils
Suggests:	biomaRt, conflicted, dplyr, edgeR, GenomicRanges, glue, knitr, rmarkdown, testthat
Published:	2022-05-16
DOI:	10.32614/CRAN.package.DGEobj
Author:	John Thompson [aut], Connie Brett [aut, cre], Isaac Neuhaus [aut], Ryan Thompson [aut]
Maintainer:	Connie Brett <connie at aggregate-genius.com>
License:	GPL-3
NeedsCompilation:	no
Language:	en-US
Materials:	README, NEWS
In views:	Omics
CRAN checks:	DGEobj results

Documentation:

Reference manual:	DGEobj.html , DGEobj.pdf
Vignettes:	DGEobj: An S3 Object to Capture and Annotate DGE Workflows (source)

Downloads:

Package source:	DGEobj_1.1.2.tar.gz
Windows binaries:	r-devel: DGEobj_1.1.2.zip, r-release: DGEobj_1.1.2.zip, r-oldrel: DGEobj_1.1.2.zip
macOS binaries:	r-release (arm64): DGEobj_1.1.2.tgz, r-oldrel (arm64): DGEobj_1.1.2.tgz, r-release (x86_64): DGEobj_1.1.2.tgz, r-oldrel (x86_64): DGEobj_1.1.2.tgz
Old sources:	DGEobj archive

Reverse dependencies:

Reverse imports:

DGEobj.utils

Linking:

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