R Observatory: Metrics for TSGS version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TSGS

1.0.1Package record

Trait Specific Gene Selection using SVM and GA

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Sudhir SrivastavaCRAN page ↗GitHub ↗Issues ↗

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. 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: 5.2 min · r-devel-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
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-04-17
WARNING13 OK, 1 WARNING2026-04-16
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 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

2.8K

CRAN downloads in the past year

Rank #9,362 · ~8/day · ~237/mo

Releases R versions

Daily download trend is not available in this view yet.

44030 days

1K90 days

2.8K1 year

Compare downloads with other packages →

Also on78 r2u

How downloads are counted

Repository

sudhirsrivastava/tsgs ↗Account: SudhirSrivastava

0Stars

0Forks

1Open issues

0Open PRs

1Releases

7Commits

2Commit identities

7 commits · Last activity 2021-08-27 · The default branch showed an older version (1.0) than CRAN on 2026-10-18

Responsiveness

not measured

Releases over time

2021-08-11 · 12026-07-07 · 1

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/sudhirsrivastava/tsgs on 2026-10-18.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing TSGS adds 66 packages (36 with compiled code, 49 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Sudhir Srivastava

Maintainer since 1.0 (2021), Author

K.K. Chaturvedi

Author

Md. Samir Farooqi

Author

D.C. Mishra

Author

Releases (2)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-07-07 · current release · diff ↗
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
1.0
record
2021-09-08
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-08
Total releases: 2 / 5 yrs
License: GPL-2 | GPL-3 OSI
Download size: 43 KB

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 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 TSGS version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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