R Observatory: Metrics for NGSToolKit version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NGSToolKit

0.1.4Package record

RNA-Seq Analysis and Genome Visualization 'Shiny' Platform

0packages depend

750downloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Sona CharlesCRAN page ↗GitHub ↗Issues ↗

Interactive 'Shiny' web application for comprehensive RNA-Seq data analysis, quality control, differential expression analysis with 'DESeq2', dimensionality reduction (PCA, t-SNE, UMAP), clustering, and integrated 'JBrowse 2' genome visualization. For differential expression analysis methods, see Love (2014) doi:10.1186/s13059-014-0550-8.

Install

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

install.packages("NGSToolKit", 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("bigfacilityiisr/NGS-Tool-Kit")

Development version from bigfacilityiisr/NGS-Tool-Kit. 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-ngstoolkit

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: 7.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK5 OK2026-09-13

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4

READMEYes · 141 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3
Examples that run: 100%2 run in a plain check (2 of them under a condition)
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

750

CRAN downloads in the past year

Rank #16,423 · ~2/day · ~63/mo

Releases R versions

Daily download trend is not available in this view yet.

53630 days

75090 days

7501 year

Compare downloads with other packages →

Also on8 r2u

How downloads are counted

Repository

bigfacilityiisr/ngs-tool-kit ↗Account: bigfacilityiisr

0Stars

1Forks

0Open issues

1Open PRs

0Releases

Last activity 2026-08-01 · The default branch showed an older version (0.1.0) than CRAN on 2026-10-11

Responsiveness

not measured

Forks over time

2026-09-13 · 02026-10-18 · 1

How these are measured

PracticesBeta

Checks run against github.com/bigfacilityiisr/ngs-tool-kit on 2026-10-11.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing NGSToolKit adds 71 packages (38 with compiled code, 74 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 3 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (19)

shiny shinydashboard shinyjs (>= 2.1.0)shinycssloaders DT ggplot2 (>= 3.3.0)DESeq2 SummarizedExperiment uwot Rtsne pheatmap reshape2 RsamtoolstoolsjsonliteutilsstatsgraphicsgrDevices

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Sona Charles

Author, Maintainer since 0.1.4 (2026)

Febin T Nabeel

Author

T E Sheeja

Author

Releases (1)

0.1.4Latest
record
first seen 2026-09-12 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First seen: 2026-09-12
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Download size: 8.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("NGSToolKit")

Format

Charles, S., Nabeel, F. T., & Sheeja, T. E. (2026). NGSToolKit: RNA-Seq Analysis and Genome Visualization 'Shiny' Platform (Version 0.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.NGSToolKit

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 NGSToolKit version 0.1.4 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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