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: 1.0.3
Depends: R (≥ 3.5.0)
Imports: assertthat, magrittr, stringr, utils, GenomicRanges
Suggests: conflicted, dplyr, glue, knitr, rmarkdown, testthat, biomaRt, edgeR
Published: 2021-04-09
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
CRAN checks: DGEobj results

Downloads:

Reference manual: DGEobj.pdf
Vignettes: DGEobj: An S3 Object to Capture and Annotate DGE Workflows
Package source: DGEobj_1.0.3.tar.gz
Windows binaries: r-devel: DGEobj_1.0.3.zip, r-release: DGEobj_1.0.3.zip, r-oldrel: DGEobj_1.0.3.zip
macOS binaries: r-release: DGEobj_1.0.3.tgz, r-oldrel: not available
Old sources: DGEobj archive

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