R Observatory: Metrics for netmhc2pan version 1.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

netmhc2pan

1.3.3Package record

Interface to 'NetMHCIIpan'

0packages depend

3.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Richèl J.C. BilderbeekCRAN page ↗GitHub ↗Issues ↗

The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/ or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.

Install

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

install.packages("netmhc2pan", 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("richelbilderbeek/netmhc2pan")

Development version from richelbilderbeek/netmhc2pan. 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-netmhc2pan

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-netmhc2pan

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-netmhc2pan

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: 1.3 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 1.3.3

READMENoVignettesYes · 1 · dynamicNEWS· In the repository, left out of the releaseCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 48includes a package overview page
Examples that run: 100%24 run in a plain check
Exported functions with examples: 50%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Demo HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #11,702 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

92790 days

3.1K1 year

Compare downloads with other packages →

Also on75 r2u3 autocran

How downloads are counted

Repository

richelbilderbeek/netmhc2pan ↗Account: richelbilderbeek

3Stars

1Forks

3Open issues

0Open PRs

6Releases

303Commits

3Commit identities

License file reads as GPL-3.0 · 303 commits · Last activity 2024-07-10 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2022-08-08 · 12026-08-27 · 3

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/richelbilderbeek/netmhc2pan on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Coverage (1)

Coverage reporting

Lint, format, editor (2)

Lint workflowRStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing netmhc2pan adds 38 packages (21 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, sp 4.3 MB, seqinr 3.4 MB.

Depends (0)

none

Imports (8)

dplyr rappdirs readr seqinr sessioninfo stringr testit tibble

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Richèl J.C. Bilderbeek

Author, Maintainer since 1.3.1 (2020)

Byungkuk Min

Contributor

Lue Ping Zhao

Contributor · added in 1.3.2

Releases (3)

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
unarchivedReturned to CRAN
2023-11-09
1.3.3Latest
record
2023-11-08 · current release · diff ↗
1.3.2
record
2023-11-09 · diff ↗ ·
added 3 exports
is_on_appveyor, is_on_ci, is_on_github_actions
archivedRemoved from CRAN
2023-10-24
requires archived package 'assertive'
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
1.3.1
record
2020-11-18
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-18
Total releases: 3 / 6 yrs
License: GPL-3 OSI
Download size: 38 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("netmhc2pan")

Format

Bilderbeek, R. J. C., Min, B., & Zhao, L. P. (2026). netmhc2pan: Interface to 'NetMHCIIpan' (Version 1.3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.netmhc2pan

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 netmhc2pan version 1.3.3 [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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