R Observatory: Metrics for DGEobj version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DGEobj

1.1.2

Differential Gene Expression (DGE) Analysis Results Data Object

1packages depend

4.5Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Connie BrettFirst published 2020-12-075 releasesCRAN page ↗

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).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("DGEobj", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-dgeobj

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-DGEobj

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-DGEobj

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.58

0.0%

Coverage · measured lines

100%

Documentation · exports

4

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 758 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 100%
Return-value docs: 95%
References docs: 0%

Downloads

4.5K

CRAN downloads in the past year

Rank #8,598 · ~12/day · ~379/mo

Releases R versions

Daily download trend is not available in this view yet.

30630 days

1.1K90 days

4.5K1 year

Compare downloads with other packages →

Also on152 r2u25 autocran803 conda_forge18 c2d4u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

assertthat magrittr stringrutils

LinkingTo (0)

none

Suggests (9)

biomaRt conflicted dplyr edgeR GenomicRanges glue knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

DGEobj.utils

Code & Tests

People & History

People (4)

Maintainer (1)

Connie Brett

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.2Latest
2022-05-16 · current release · diff ↗
1.1.1
2022-05-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
2022-03-25 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.3
2021-04-09 · diff ↗
1.0.1
2020-12-07
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-07
Total releases: 5 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DGEobj")

Format

Brett, C., Neuhaus, I., Thompson, J., & Thompson, R. (2022). DGEobj: Differential Gene Expression (DGE) Analysis Results Data Object (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.DGEobj

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for DGEobj version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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