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>.
| Version: | 0.1.4 |
| 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) |
| Published: | 2026-09-12 |
| DOI: | 10.32614/CRAN.package.NGSToolKit (may not be active yet) |
| Author: | Sona Charles [aut, cre], Febin T Nabeel [aut], T E Sheeja [aut] |
| Maintainer: | Sona Charles <sonacharlesicar at gmail.com> |
| BugReports: | https://github.com/bigfacilityiisr/NGS-Tool-Kit/issues |
| License: | GPL-3 |
| URL: | https://github.com/bigfacilityiisr/NGS-Tool-Kit |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | NGSToolKit results |
| Reference manual: | NGSToolKit.html , NGSToolKit.pdf |
| Package source: | NGSToolKit_0.1.4.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): NGSToolKit_0.1.4.tgz, r-release (x86_64): NGSToolKit_0.1.4.tgz, r-oldrel (x86_64): NGSToolKit_0.1.4.tgz |
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