R Observatory: Metrics for epitopeR version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2023-06-11. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.0.0, its last release before removal.

epitopeR

1.0.0

Predict Peptide-MHC Binding

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Joan Zhang1 releasesCRAN page ↗

A suite of tools to predict peptide MHC (major histocompatibility complex) presentation in the context of both human and mouse. Polymorphic peptides between self and foreign proteins are identified. The ability of peptides to bind self MHC is assessed and scored. Based on half maximal inhibitory concentration as queried through the immune epitope database API http://tools.iedb.org using user defined methods, the foreign peptides most likely to be presented are output along with their predicted binding strength, amino acid position, the protein from which each peptide was derived, and the presenting allele. "References:" Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. doi:10.1093/nar/gky1006.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/epitopeR/epitopeR_1.0.0.tar.gz"
pkgFile <- "epitopeR_1.0.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-epitoper

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

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.04

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 79%
Return-value docs: 100%
References docs: 0%

Downloads

epitopeR Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on84 r2u

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (13)

dplyr fs httr janitor purrr rlang stringr tibble tidyverseutilsreadr Biostrings seqinr

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat ggseqlogo ggVennDiagram

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Joan Zhang

Author, Maintainer

Authors (3)

Joan Zhang

Author, Maintainer

Aileen Johnson

Author

Christian P Larsen

Copyright holder, Author

Copyright holders (1)

Christian P Larsen

Copyright holder, Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-06-11
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
1.0.0
2023-02-15
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 1
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epitopeR")

Format

Zhang, J., Johnson, A., & Larsen, C. P. (n.d.). epitopeR: Predict Peptide-MHC Binding (Version 1.0.0) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=epitopeR

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 epitopeR version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →