R Observatory: Metrics for SequenceAnalysis version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2018-07-29. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.3, its last release before removal.

SequenceAnalysis

1.3Package record

Sequence Analysis

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Babak KhorsandCRAN page ↗

Provides: 1) By Giving UniProtKB, the Protein Sequence will be returned from UniProt database. 2)By Giving UniProtKB, the Nucleotide Sequence will be returned from EBI database. 3) Amino acid Composition is calculated by four different methods: a) Twenty-two independent categories are considered, with one amino acid for each category. B) Five categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged) are considered according to the standard chemical structures of amino acids. c) Six categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged, Special cases) are considered which Cysteine, Selenocysteine, Glycine and Proline are placed in Special cases group. d)Eight categories are clustered via k-means algorithm on Physicochemical index of amino acids. 4) GC Content: Percentage of nucleotide g and c in sequence. 5) Codon usage: Frequency of occurrence of synonymous codons. 6) Stacking Energy: The NN model for nucleic acids assumes that the stability of a given base pair depends on the identity and orientation of neighboring base pairs. Stacking Energy = DeltaG(total) = Sigma (n(i)*DeltaG(i)) + DeltaG(init) + DeltaG(end) + DeltaG(sym), which DeltaG for i, init and end is obtained by Unified NN free energy parameter. Symmetry of self-complementary duplexes is also included by DeltaG(sym) equals to +0.43 (kcal/mol) if the duplex is self-complementary and zero if it is non-self-complementary. 7) Complement of desired nucleotide sequence. 8) Reverse of desired nucleotide sequence. 9) Reverse-Complement of desired nucleotide sequence. 10) Protein, Gene and Organism of desired UniProt ID. 11) Converting nucleotide sequence to protein sequence. 12) Getting Localization From Gene Ontology Cellular Component inside Uniprot. 13) All related codons of desired amino acid.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/SequenceAnalysis/SequenceAnalysis_1.3.tar.gz"
pkgFile <- "SequenceAnalysis_1.3.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 (1.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 100%13 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

SequenceAnalysis Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (2)

R >= 2.10.0XML

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Babak Khorsand

Author, Maintainer since 1.2 (2016)

Javad Zahiri

Thesis advisor

Abdorreza Savadi

Thesis advisor

Releases (2)

Pick two releases to compare their code metrics.

R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2018-07-29
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.3
record
2016-08-15 · diff ↗ ·
added 3 exports
SequenceAnalysis.AminoAcidToCodon, SequenceAnalysis.CodonToAminoAcid, SequenceAnalysis.GetLocalization
1.2
record
2016-08-10
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-08-10
Total releases: 2 / 10 yrs
License: GPL
Minimum R: ≥ 2.10.0

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SequenceAnalysis")

Format

Khorsand, B., Zahiri, J., & Savadi, A. (n.d.). SequenceAnalysis: Sequence Analysis (Version 1.3) [Computer software]. Retrieved October 26, 2026, from https://CRAN.R-project.org/package=SequenceAnalysis

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 SequenceAnalysis version 1.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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