R Observatory: Metrics for DGEobj version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DGEobj

1.1.2Package record

Differential Gene Expression (DGE) Analysis Results Data Object

1packages depend

4.6Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Connie BrettCRAN 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).

Changes in 1.1.2

Made all Bioconductor packages optional (suggested)
Added a new, minimal "mini" example object that has no internal Bioconductor-based features (ie normalization, analysis) to allow

for clean, simple examples that do not depend on suggested packages

Testing updated so that when Bioconductor suggested packages are unavailable the tests will not be run

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMEYes · 758 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.1.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 27includes a package overview page
Examples that run: 91%21 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (1)

DGEobj: An S3 Object to Capture and Annotate DGE Workflows

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #6,635 · ~13/day · ~384/mo

Releases R versions

Daily download trend is not available in this view yet.

50830 days

1.3K90 days

4.6K1 year

Compare downloads with other packages →

Also on155 r2u9 autocran708 conda_forge46 c2d4u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing DGEobj adds 9 packages (6 with compiled code, 14 MB of source tarballs). Heaviest: stringi 11 MB, vctrs 1.0 MB, rlang 766 KB.

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

Imports 1

Depends, Imports or LinkingTo, most downloaded first

DGEobj.utils

How these are counted

Code & Tests

People & History

People (4)

Connie Brett

Author, Maintainer since 1.0.1 (2020)

Isaac Neuhaus

Author

John Thompson

Author

Ryan Thompson

Author

Releases (5)

Pick two releases to compare their code metrics.

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
record
2022-05-16 · current release · diff ↗
1.1.1
record
2022-05-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2022-03-25 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.3
record
2021-04-09 · diff ↗ ·
removed 3 exports
getAttribute, rmItems, setAttribute

added 1 export
initDGEobjDef
1.0.1
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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