ampir

1.1.0

Predict Antimicrobial Peptides

0packages depend

4Kdownloads / year

98.7%test coverage

11/13checks pass

Overview

About

Maintained by Legana FingerhutFirst published 2019-12-063 releasesCRAN page ↗GitHub ↗

A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale. It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated physico-chemical and compositional sequence properties described in Meher et al. (2017) doi:10.1038/srep42362. In order to support genome-wide analyses, these models are designed to accept any type of protein as input and calculation of compositional properties has been optimised for high-throughput use. For best results it is important to select the model that accurately represents your sequence type: for full length proteins, it is recommended to use the default "precursor" model. The alternative, "mature", model is best suited for mature peptide sequences that represent the final antimicrobial peptide sequence after post-translational processing. For details see Fingerhut et al. (2020) doi:10.1093/bioinformatics/btaa653. The 'ampir' package is also available via a Shiny based GUI at https://ampir.marine-omics.net/.

Install

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

install.packages("ampir", 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("Legana/ampir")

Development version from Legana/ampir. 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-ampir

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-ampir

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-ampir

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 5.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 1.13

98.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-30
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-03-10
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 494 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

CRAN downloads in the past year

Rank #10,259 · ~11/day · ~332/mo

Releases R versions

Daily download trend is not available in this view yet.

35630 days

1K90 days

4K1 year

Compare downloads with other packages →

Also on442 r2u55 autocran3.2K conda_forge31 c2d4u

Repository

GitHub ↗ legana/ampir

36Stars

6Forks

0Open issues

0Open PRs

0Releases

240Commits

5Contributors

240 commits · Last activity 2024-12-17 · 0% stars, 30d

Stars over time

2025-07-25 · 332026-07-07 · 36

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/legana/ampir on 2026-07-30.

Continuous integration (1)

Travis CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (5)

Peptides caret kernlab Rcppparallel

LinkingTo (1)

Rcpp

Suggests (4)

testthat knitr rmarkdown e1071

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Legana Fingerhut

Author, Maintainer

Authors (2)

Legana Fingerhut

Author, Maintainer

Ira Cooke

Author

Contributors (2)

Nan Xiao

Contributor

Jinlong Zhang

Contributor

Package Timeline

3 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
R
R 4.2.0 released · 2022-04-22
1.1.0Latest
2021-06-29 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.0
2020-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.0
2019-12-06
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-06
Total releases: 3 / 7 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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