| Type: | Package |
| Title: | RNA-Seq Analysis and Genome Visualization 'Shiny' Platform |
| Version: | 0.1.4 |
| Author: | Sona Charles [aut, cre], Febin T Nabeel [aut], T E Sheeja [aut] |
| Maintainer: | Sona Charles <sonacharlesicar@gmail.com> |
| 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. For differential expression analysis methods, see Love (2014) <doi:10.1186/s13059-014-0550-8>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Depends: | R (≥ 4.0.0) |
| Imports: | shiny (≥ 1.7.0), shinydashboard (≥ 0.7.0), shinyjs (≥ 2.1.0), shinycssloaders (≥ 1.0.0), DT (≥ 0.20), ggplot2 (≥ 3.3.0), DESeq2, SummarizedExperiment, uwot, Rtsne, pheatmap, reshape2, Rsamtools, tools, jsonlite, utils, stats, graphics, grDevices |
| Suggests: | testthat (≥ 3.0.0) |
| URL: | https://github.com/bigfacilityiisr/NGS-Tool-Kit |
| BugReports: | https://github.com/bigfacilityiisr/NGS-Tool-Kit/issues |
| Config/roxygen2/version: | 8.0.0 |
| NeedsCompilation: | no |
| RoxygenNote: | 7.3.3 |
| Packaged: | 2026-09-03 02:43:47 UTC; Febin T Nabeel |
| Repository: | CRAN |
| Date/Publication: | 2026-09-12 13:40:22 UTC |
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.