R Observatory: Metrics for PSSMCOOL version 0.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PSSMCOOL

0.2.4Package record

Features Extracted from Position Specific Scoring Matrix (PSSM)

0packages depend

2.9Kdownloads / year

96.0%test coverage

13/13flavors OK

Overview

About

Maintained by Alireza mohammadiCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
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 0.2.4

READMEYes · 5,687 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 40includes a package overview page
Examples that run: 100%39 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 90%

Vignettes (1)

PSSMCOOL

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #16,328 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

26030 days

76690 days

2.9K1 year

Compare downloads with other packages →

Also on90 r2u5 autocran38 c2d4u

How downloads are counted

Repository

biocool-lab/pssmcool ↗Account: BioCool-Lab

4Stars

5Forks

1Open issues

0Open PRs

0Releases

59Commits

2Commit identities

59 commits · Last activity 2021-12-30 · The default branch showed an older version (0.2.2) than CRAN on 2026-10-22

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/biocool-lab/pssmcool on 2026-10-22.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing PSSMCOOL adds 4 packages (2 with compiled code, 425 KB of source tarballs). Heaviest: gtools 236 KB, phonTools 178 KB, infotheo 8.1 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Alireza mohammadi

Author, Maintainer since 0.1.0 (2020)

Saber mohammadi

Author · added in 0.2.2

Javad zahiri

Author · added in 0.2.1

Releases (6)

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.2.4Latest
record
2022-01-04 · current release · diff ↗ ·
removed 5 exports
AATP_TPCC, DPC_PSSM, EDP_MEDP, PSSMAC, k_seperated_bigrame

added 8 exports
AATP_TPC, EDP_EEDP_MEDP, RPM_PSSM, aac_pssm, aadp_pssm, dpc_pssm, k_separated_bigrams_pssm, pssm_composition
0.2.3
record
2021-12-11 · diff ↗
0.2.2
record
2021-09-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.1
record
2020-10-25 · diff ↗
0.2.0
record
2020-08-07 · diff ↗ ·
added 3 exports
k_mers, scsh2, three_mer
0.1.0
record
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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PSSMCOOL")

Format

mohammadi, A., mohammadi, S., & zahiri, J. (2022). PSSMCOOL: Features Extracted from Position Specific Scoring Matrix (PSSM) (Version 0.2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.PSSMCOOL

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 PSSMCOOL version 0.2.4 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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