protr

1.7-5

Generating Various Numerical Representation Schemes for Protein Sequences

0packages depend

10.5Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Nan XiaoFirst published 2012-11-1829 releasesCRAN page ↗GitHub ↗

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) DOI:10.1093/bioinformatics/btv042. For full functionality, the software 'ncbi-blast+' is needed, see https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html for more information.

Install

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

install.packages("protr", 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("nanxstats/protr")

Development version from nanxstats/protr. 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-protr

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-protr

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-protr

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 472 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 96%
Return-value docs: 100%
References docs: 34%

Downloads

10.5K

CRAN downloads in the past year

Rank #5,450 · ~29/day · ~878/mo

Releases R versions

Daily download trend is not available in this view yet.

39330 days

1.6K90 days

10.5K1 year

Compare downloads with other packages →

Also on117 r2u4 autocran2.5K conda_forge23 c2d4u

Repository

GitHub ↗ nanxstats/protr

53Stars

13Forks

5Open issues

0Open PRs

18Releases

343Commits

5Contributors

protein-sequencesfeature-extractionmachine-learningbioinformaticsfeature-engineeringpeptidessequence-analysis

343 commits · Last activity 2025-08-25 · +1.9% stars, 30d

Stars over time

2024-06-10 · 512026-07-07 · 53

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/nanxstats/protr on 2026-07-31.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.2

Imports (0)

none

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown Biostrings GOSemSim foreach doParallel org.Hs.eg.db

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Nan Xiao

Author, Maintainer · added in 0.2-0

Authors (3)

Nan Xiao

Author, Maintainer · added in 0.2-0

Dong-Sheng Cao

Author · added in 1.4-0

Qing-Song Xu

Author · added in 1.4-0

Contributors (1)

Sebastian Mueller

Contributor · added in 1.7-0

Listed in earlier versions (3)

Dongsheng Cao

no longer listed · 0.1-0 to 1.3-0

Yizeng Liang

no longer listed · 0.1-0 to 2.15.3

Qingsong Xu

no longer listed · 0.1-0 to 1.3-0

Package Timeline

29 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.7-5Latest
2025-08-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.7-4
2024-09-12 · diff ↗
1.7-3
2024-08-30 · diff ↗
1.7-2
2024-07-21 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.7-1
2024-04-20 · diff ↗
1.7-0
2023-10-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6-3
2023-03-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.6-2
2019-05-18 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 28 earlier events

1.6-1
2019-02-24 · diff ↗
1.6-0
2019-02-11 · diff ↗
1.5-2
2018-11-22 · diff ↗
1.5-1
2018-07-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.5-0
2017-11-18 · diff ↗
1.4-2
2017-09-29 · diff ↗
1.4-1
2017-07-09 · diff ↗
1.4-0
2017-06-06 · diff ↗
1.3-0
2017-05-08 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.2-1
2016-12-30 · diff ↗
1.2-0
2016-11-12 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1-1
2015-12-29 · diff ↗
1.0-1
2015-11-27 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.5-1
2014-12-24 · diff ↗
0.4-1
2014-10-10 · diff ↗
0.3-1
2014-08-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
3.0.3
2014-01-25 · diff ↗
0.2-1
2014-01-25 · diff ↗
0.2-0
2013-12-19 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.15.3
2012-11-18 · diff ↗
0.1-0
2012-11-18
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-11-18
Total releases: 29 / 14 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.0.2
Bundled data: 228 KB / 35 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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