Package 'NGSToolKit'

Title: RNA-Seq Analysis and Genome Visualization Shiny Platform
Description: 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.
Authors: Sona Charles [aut, cre], Febin T Nabeel [aut]
Maintainer: Sona Charles <sonacharlesicar@gmail.com>
License: GPL-3
Version: 0.1.0
Built: 2026-10-14 08:03:47 UTC
Source: https://github.com/bigfacilityiisr/ngs-tool-kit

Help Index

Run the NGS Tool Kit Application (Alias)

Description

Run the NGS Tool Kit Application (Alias)

Usage

run_app(launch.browser = TRUE, port = NULL, host = "127.0.0.1")

Arguments

launch.browser

Logical, whether to open the application in a web browser. Default is TRUE.
port

Optional port number for running the Shiny server. Default is NULL.
host

Optional host IP address. Default is "127.0.0.1".

Value

Launches the Shiny application.

Examples

if (interactive()) {
  run_app()
}

Run the NGS Tool Kit Shiny Application

Description

Launches the interactive Shiny web application for RNA-Seq data analysis, differential expression, clustering, and genome visualization.

Usage

run_ngs_toolkit(launch.browser = TRUE, port = NULL, host = "127.0.0.1")

Arguments

launch.browser

Logical, whether to open the application in a web browser. Default is TRUE.
port

Optional port number for running the Shiny server. Default is NULL.
host

Optional host IP address. Default is "127.0.0.1".

Value

Launches the Shiny application.

Examples

if (interactive()) {
  run_ngs_toolkit()
}

Setup and verify JBrowse assets

Description

Initializes the local user data directory for JBrowse sessions in a CRAN-compliant manner.

Usage

setup_jbrowse(target_dir = NULL)

Arguments

target_dir

Path to store JBrowse user data. Defaults to user data directory.

Value

Logical indicating success.