AmpGram

1.0

Prediction of Antimicrobial Peptides

0packages depend

3.3Kdownloads / year

5.1%test coverage

13/13checks pass

Overview

About

Maintained by Michal BurdukiewiczFirst published 2020-05-311 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.01

5.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 257 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 80%
References docs: 13%

Downloads

3.3K

CRAN downloads in the past year

Rank #12,603 · ~9/day · ~271/mo

Releases R versions

Daily download trend is not available in this view yet.

28430 days

84990 days

3.3K1 year

Compare downloads with other packages →

Also on104 r2u31 autocran

Repository

GitHub ↗ michbur/ampgram

4Stars

1Forks

0Open issues

0Open PRs

0Releases

81Commits

4Contributors

81 commits · Last activity 2022-02-28

Stars over time

2023-02-27 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/michbur/ampgram on 2026-07-19.

Continuous integration (1)

Travis CI

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

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

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 313 (59%)Rd 214 (41%)

Code characteristics

Object systems

S31

Cyclomatic complexity: 1.0 median / 9 max

Test coverage

Line coverage

Expression

7.0%

Tests / Examples

5.1% / 20% ex

Functions

12 5 exported

Complexity

2.3 avg / 9 max

Call network

12 nodes / 9 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

12 functions

Function	Cyclo	Coverage
AmpGram_gui exp	1	0%
get_AMPs exp	1	0%
install_AmpGramModel exp	1	0%
pred2df exp	1	0%
read_txt exp	9	0%
calculate_statistics	1	0%

People & History

People (6)

Maintainer (1)

Michal Burdukiewicz

Maintainer, Author

Authors (2)

Michal Burdukiewicz

Maintainer, Author

Dominik Rafacz

Author

Contributors (4)

Contributor

Contributor

Contributor

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

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
Installed size: not tracked yet
With dependencies: not tracked yet

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