R Observatory: Metrics for AmpGram version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AmpGram needs biogram, which CRAN will archive unless its check problems are fixed by Nov 2.

AmpGram

1.0Package record

Prediction of Antimicrobial Peptides

0packages depend

3.3Kdownloads / year

5.1%test coverage

13/13flavors OK

Overview

About

Maintained by Michal BurdukiewiczCRAN page ↗GitHub ↗Issues ↗

Predicts antimicrobial peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI. The AmpGram model is too large for CRAN and it has to be downloaded separately from the repository: https://github.com/michbur/AmpGramModel.

Install

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

install.packages("AmpGram", 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("michbur/AmpGram")

Development version from michbur/AmpGram. 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-ampgram

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-AmpGram

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-AmpGram

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: 2.2 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 1.0

READMEYes · 257 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 60%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 13%

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #11,483 · ~9/day · ~276/mo

Releases R versions

Daily download trend is not available in this view yet.

32930 days

93790 days

3.3K1 year

Compare downloads with other packages →

Also on108 r2u22 autocran

How downloads are counted

Repository

michbur/ampgram ↗Account: michbur

4Stars

1Forks

0Open issues

0Open PRs

0Releases

81Commits

4Commit identities

81 commits · Last activity 2022-02-28 · Default branch at 1.1, ahead of CRAN 1.0 (checked 2026-10-18)

Responsiveness

not measured

Stars over time

2023-02-27 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/michbur/ampgram on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing AmpGram adds 108 packages (53 with compiled code, 62 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, pak 3.8 MB.

Depends (1)

R >= 3.5.0

Imports (6)

biogram devtools pbapply ranger shiny stringi

LinkingTo (0)

none

Suggests (6)

DT ggplot2 pander rmarkdown shinythemes spelling

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

biogramfix by Nov 2

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Michal Burdukiewicz

Maintainer since 1.0 (2020), Author

Author

Contributor

Contributor

Contributor

Contributor

Releases (1)

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0Latest
record
2020-05-31 · current release
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-31
Total releases: 1 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.4 KB / 1 file
Download size: 60 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AmpGram")

Format

Burdukiewicz, M., Chilimoniuk, J., Pietluch, F., Rafacz, D., Roediger, S., & Sidorczuk, K. (2020). AmpGram: Prediction of Antimicrobial Peptides (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.AmpGram

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 AmpGram version 1.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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