PSSMCOOL

0.2.4

Features Extracted from Position Specific Scoring Matrix (PSSM)

0packages depend

2.9Kdownloads / year

96.0%test coverage

13/13checks pass

Overview

About

Maintained by Alireza mohammadiFirst published 2020-05-086 releasesCRAN page ↗GitHub ↗

Returns almost all features that has been extracted from Position Specific Scoring Matrix (PSSM) so far, which is a matrix of L rows (L is protein length) and 20 columns produced by 'PSI-BLAST' which is a program to produce PSSM Matrix from multiple sequence alignment of proteins see https://www.ncbi.nlm.nih.gov/books/NBK2590/ for mor details. some of these features are described in Zahiri, J., et al.(2013) DOI:10.1016/j.ygeno.2013.05.006, Saini, H., et al.(2016) DOI:10.17706/jsw.11.8.756-767, Ding, S., et al.(2014) DOI:10.1016/j.biochi.2013.09.013, Cheng, C.W., et al.(2008) DOI:10.1186/1471-2105-9-S12-S6, Juan, E.Y., et al.(2009) DOI:10.1109/CISIS.2009.194.

Install

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

install.packages("PSSMCOOL", 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("BioCool-Lab/PSSMCOOL")

Development version from BioCool-Lab/PSSMCOOL. 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-pssmcool

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-PSSMCOOL

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-PSSMCOOL

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

96.0%

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 · 5,687 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

2.9K

CRAN downloads in the past year

Rank #14,345 · ~8/day · ~242/mo

Releases R versions

Daily download trend is not available in this view yet.

25830 days

76990 days

2.9K1 year

Compare downloads with other packages →

Also on113 r2u34 autocran25 c2d4u

Repository

GitHub ↗ biocool-lab/pssmcool

4Stars

5Forks

1Open issues

0Open PRs

0Releases

59Commits

2Contributors

59 commits · Last activity 2021-12-30

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/biocool-lab/pssmcool on 2026-07-19.

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 >= 3.1.0

Imports (5)

utilsgtools infotheo phonTools dtt

LinkingTo (0)

none

Suggests (5)

testthat spelling waveslim knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,625 (34%)Other 2,436 (32%)Rd 1,243 (16%)Vignettes 1,186 (15%)CSS 214 (3%)

Code characteristics

Cyclomatic complexity: 6.0 median / 22 max
Test cases: 34 / 0.10 per code line

Test coverage

Line coverage

96%

Expression

96.1%

Tests / Examples

96.0% / 96% ex

Functions

39 39 exported

Complexity

6.6 avg / 22 max

Call network

39 nodes / 5 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

39 functions

Function	Cyclo	Coverage
FPSSM2 exp	5	53%
smoothed_PSSM exp	10	70%
disulfid exp	9	86%
k_mers exp	5	90%
three_mer exp	3	94%
kiderafactor exp	10	95%

People & History

People (3)

Maintainer (1)

Alireza mohammadi

Author, Maintainer

Authors (3)

Alireza mohammadi

Author, Maintainer

Saber mohammadi

Author · added in 0.2.2

Javad zahiri

Author · added in 0.2.1

Package Timeline

6 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
0.2.4Latest
2022-01-04 · current release · diff ↗
0.2.3
2021-12-11 · diff ↗
0.2.2
2021-09-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.1
2020-10-25 · diff ↗
0.2.0
2020-08-07 · diff ↗
0.1.0
2020-05-08
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-08
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 2.5 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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