NGSToolKit: RNA-Seq Analysis Platform and JBrowse Visualization

NGSToolKit is an R Shiny application for comprehensive RNA-Seq data exploration, quality control, differential expression analysis (DESeq2), clustering, dimensionality reduction (t-SNE, UMAP, PCA), and integrated genomic visualization using JBrowse 2.

Installation

You can install NGSToolKit directly from CRAN or GitHub:

# Install from CRAN (once published):
install.packages("NGSToolKit")

# Or install development version from GitHub:
# install.packages("remotes")
remotes::install_github("bigfacilityiisr/NGS-Tool-Kit")

Quick Start

Launch the application using:

library(NGSToolKit)

# Launch the Shiny interface in your default browser:
run_ngs_toolkit()

Features

• Data QC & Exploration: Summary statistics, library sizes, and count distributions.
• Differential Expression: Powered by DESeq2 with customizable thresholds, volcano plots, and MA plots.
• Dimensionality Reduction: PCA, t-SNE, and UMAP interactive visual projections.
• Clustering & Heatmaps: Hierarchical clustering, correlation matrices, and custom heatmaps.
• Integrated JBrowse 2: Interactive genome browser supporting FASTA, GFF3, BAM, and VCF files.

Authors & Institution

• ICAR – Indian Institute of Spices Research, Kozhikode, Kerala, India
• Contact: sonacharlesicar@gmail.com, nabeelfebin@gmail.com