GeneTonic
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Bioconductor version: 3.23 · Package version: 3.6.0
This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GeneTonic")Details
| Maintainer | Federico Marini <marinif@uni-mainz.de> |
| Author | Federico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>), Annekathrin Nedwed [aut] (ORCID: <https://orcid.org/0000-0002-2475-4945>), Edoardo Filippi [ctb] (ORCID: <https://orcid.org/0009-0003-9858-0137>) |
| License | MIT + file LICENSE |
| URL | https://github.com/federicomarini/GeneTonic |
| Bug Reports | https://github.com/federicomarini/GeneTonic/issues |
| Downloads rank | 402 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ReportWriting, ShinyApps, Software, Transcription, Transcriptomics, Visualization |
Documentation
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Dependencies
Depends: R (>= 4.0.0)
Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork
Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0)