R Observatory: Metrics for GenomicSig version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenomicSig

0.1.0Package record

Computation of Genomic Signatures

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Anu SharmaCRAN page ↗

Genomic signatures represent unique features within a species' DNA, enabling the differentiation of species and offering broad applications across various fields. This package provides essential tools for calculating these specific signatures, streamlining the process for researchers and offering a comprehensive and time-saving solution for genomic analysis.The amino acid contents are identified based on the work published by Sandberg et al. (2003) doi:10.1016/s0378-1119(03)00581-x and Xiao et al. (2015) doi:10.1093/bioinformatics/btv042. The Average Mutual Information Profiles (AMIP) values are calculated based on the work of Bauer et al. (2008) doi:10.1186/1471-2105-9-48. The Chaos Game Representation (CGR) plot visualization was done based on the work of Deschavanne et al. (1999) doi:10.1093/oxfordjournals.molbev.a026048 and Jeffrey et al. (1990) doi:10.1093/nar/18.8.2163. The GC content is calculated based on the work published by Nakabachi et al. (2006) doi:10.1126/science.1134196 and Barbu et al. (1956) https://pubmed.ncbi.nlm.nih.gov/13363015. The Oligonucleotide Frequency Derived Error Gradient (OFDEG) values are computed based on the work published by Saeed et al. (2009) doi:10.1186/1471-2164-10-S3-S10. The Relative Synonymous Codon Usage (RSCU) values are calculated based on the work published by Elek (2018) https://urn.nsk.hr/urn:nbn:hr:217:686131.

Install

R (CRAN)Ubuntu (r2u)

install.packages("GenomicSig", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-genomicsig

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.2 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 0.1.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 86%

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #20,777 · ~6/day · ~168/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

64390 days

2K1 year

Compare downloads with other packages →

Also on69 r2u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing GenomicSig adds 31 packages (16 with compiled code, 40 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, sp 4.3 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.5.0

Imports (5)

kaos Biostringsstatsentropy seqinr

LinkingTo (0)

none

Suggests (0)

none

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 (11)

Anu Sharma

Author, Maintainer since 0.1.0 (2024)

Dwijesh Chandra Mishra

Author

Author

Author

Author

Author

Sayanti Guha Majumdar

Author

Author

Author

Contributor

Contributor

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0Latest
record
2024-09-11 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-11
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.2 KB / 1 file
Download size: 17 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GenomicSig")

Format

Anu Sharma, Dwijesh Chandra Mishra, Girish Kumar Jha, Mailarlinga, Megha Garg, Sanjeev Kumar, Sayanti Guha Majumdar, Sharanbasappa, Shashi Bhushan Lal, Sudhir Srivastava, & S, K. (2024). GenomicSig: Computation of Genomic Signatures (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.GenomicSig

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 GenomicSig version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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