R Observatory: Metrics for TSGS version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TSGS

1.0.1

Trait Specific Gene Selection using SVM and GA

0packages depend

2.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Sudhir SrivastavaFirst published 2021-09-082 releasesCRAN page ↗GitHub ↗

Obtaining relevant set of trait specific genes from gene expression data is important for clinical diagnosis of disease and discovery of disease mechanisms in plants and animals. This process involves identification of relevant genes and removal of redundant genes as much as possible from a whole gene set. This package returns the trait specific gene set from the high dimensional RNA-seq count data by applying combination of two conventional machine learning algorithms, support vector machine (SVM) and genetic algorithm (GA). GA is used to control and optimize the subset of genes sent to the SVM for classification and evaluation. Genetic algorithm uses repeated learning steps and cross validation over number of possible solution and selects the best. The algorithm selects the set of genes based on a fitness function that is obtained via support vector machines. Using SVM as the classifier performance and the genetic algorithm for feature selection, a set of trait specific gene set is obtained.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("TSGS", 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("SudhirSrivastava/TSGS")

Development version from SudhirSrivastava/TSGS. 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-tsgs

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

Health

CRAN checks

13OK

Slowest check: 5.1 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-17
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-04-16
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #14,913 · ~7/day · ~203/mo

Releases R versions

Daily download trend is not available in this view yet.

23730 days

71490 days

2.4K1 year

Compare downloads with other packages →

Also on103 r2u

Repository

GitHub ↗ sudhirsrivastava/tsgs

0Stars

0Forks

1Open issues

0Open PRs

1Releases

7Commits

2Contributors

7 commits · Last activity 2021-08-27

Releases over time

2021-08-11 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/sudhirsrivastava/tsgs on 2026-08-23.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

caret edgeR fastmatch genalg kernlab e1071

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Sudhir Srivastava

Maintainer, Author

Authors (4)

Maintainer, Author

Author

Author

Author

Package Timeline

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

1.0.1Latest
2026-07-07 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-09-08
Total releases: 2 / 5 yrs
License: GPL-2 | GPL-3 OSI
Download size: 43 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TSGS")

Format

Srivastava, S., Chaturvedi, K. K., Farooqi, M. S., & Mishra, D. C. (2026). TSGS: Trait Specific Gene Selection using SVM and GA (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.TSGS

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 TSGS version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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