TGS

1.0.1

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Saptarshi PyneFirst published 2018-11-162 releasesCRAN page ↗GitHub ↗

Rapid advancements in high-throughput gene sequencing technologies have resulted in genome-scale time-series datasets. Uncovering the underlying temporal sequence of gene regulatory events in the form of time-varying gene regulatory networks demands accurate and computationally efficient algorithms. Such an algorithm is 'TGS'. It is proposed in Saptarshi Pyne, Alok Ranjan Kumar, and Ashish Anand. Rapid reconstruction of time-varying gene regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(1):278{291, Jan-Feb 2020. The TGS algorithm is shown to consume only 29 minutes for a microarray dataset with 4028 genes. This package provides an implementation of the TGS algorithm and its variants.

Install

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

install.packages("TGS", 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("sap01/TGS")

Development version from sap01/TGS. 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-tgs

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

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 1.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 141 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.4K

CRAN downloads in the past year

Rank #16,478 · ~6/day · ~196/mo

Releases R versions

Daily download trend is not available in this view yet.

20630 days

69790 days

2.4K1 year

Compare downloads with other packages →

Also on85 r2u16 c2d4u

Repository

GitHub ↗ sap01/tgs

0Stars

0Forks

0Open issues

0Open PRs

2Releases

57Commits

2Contributors

57 commits · Last activity 2020-05-22

Releases over time

2020-05-07 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/sap01/tgs on 2026-07-19.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

rjson bnstruct ggm foreach doParallel minet

LinkingTo (0)

none

Suggests (4)

R.rsp testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Saptarshi Pyne

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

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
R
R 4.1.0 released · 2021-05-18
1.0.1Latest
2020-05-07 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.0
2018-11-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-16
Total releases: 2 / 8 yrs
License: CC BY-NC-SA 4.0
Download size: 114 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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