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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.pdf
Vignettes: DGEobj: An S3 Object to Capture and Annotate DGE Workflows

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:

Please use the canonical form https://CRAN.R-project.org/package=DGEobj to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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