R Observatory: Metrics for autoGO version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

autoGO

1.0.3

Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

0packages depend

3.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Fabio TicconiFirst published 2023-01-164 releasesCRAN page ↗GitHub ↗

Auto-GO is a framework that enables automated, high quality Gene Ontology enrichment analysis visualizations. It also features a handy wrapper for Differential Expression analysis around the 'DESeq2' package described in Love et al. (2014) doi:10.1186/s13059-014-0550-8. The whole framework is structured in different, independent functions, in order to let the user decide which steps of the analysis to perform and which plot to produce.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mpallocc/auto-go")

Development version from mpallocc/auto-go. Installs pak first if it is not already available.

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-autogo

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

Health

CRAN checks

13OK

Slowest check: 10.9 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

24

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
OK2026-07-26
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-19
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 14 earlier snapshots

ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-20
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-16
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-25
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-03-21
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 10%
Documented parameters: 100%
Return-value docs: 91%
References docs: 0%

Downloads

3.7K

CRAN downloads in the past year

Rank #9,626 · ~10/day · ~311/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

98890 days

3.7K1 year

Compare downloads with other packages →

Also on229 r2u

Repository

GitHub ↗ mpallocc/auto-go

3Stars

2Forks

2Open issues

1Open PRs

6Releases

93Commits

4Contributors

93 commits · Last activity 2025-08-05

Stars over time

2025-06-23 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/mpallocc/auto-go on 2026-08-23.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.5.0readr dplyr enrichR (>= 3.4)

Imports (21)

ape ComplexHeatmap DESeq2 dichromat ggplot2 ggrepelgrDevicesGSVA msigdbr openxlsx purrr RColorBrewer reshape2statsstringr SummarizedExperiment textshape tibble tidyr tidyselectutils

LinkingTo (0)

none

Suggests (3)

knitr rlang rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Fabio Ticconi

Maintainer

Authors (5)

Author

Author

Author

Author

Author

Listed in earlier versions (1)

Lorenzo D\

no longer listed · 0.9 to 1.0.3

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
2025-08-20 · current release · diff ↗
unarchivedReturned to CRAN
2025-08-20
archivedRemoved from CRAN
2025-07-10
requires archived package 'imguR'
R
R 4.5.0 released · 2025-04-11
1.0.1
2025-02-27 · diff ↗
unarchivedReturned to CRAN
2025-02-27
archivedRemoved from CRAN
2024-11-04
requires archived package 'enricheR'
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.9.1
2023-02-13 · diff ↗
0.9
2023-01-16
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-16
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 737 KB / 3 files
Download size: 3.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("autoGO")

Format

Ticconi, F., D'Ambrosio, L., Grassucci, I., Massacci, A., Pallocca, M., & Sperandio, E. (2025). autoGO: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.autoGO

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 autoGO version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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