GeneTonic

DOI: 10.18129/B9.bioc.GeneTonic  

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Bioconductor version: Release (3.17)

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.

Author: Federico Marini [aut, cre] , Annekathrin Ludt [aut]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GeneTonic")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GeneTonic")

 

HTML	R Script	The GeneTonic User's Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ReportWriting, ShinyApps, Software, Transcription, Transcriptomics, Visualization
Version	2.4.2
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	MIT + file LICENSE
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, ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork
LinkingTo
Suggests	knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/federicomarini/GeneTonic
BugReports	https://github.com/federicomarini/GeneTonic/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GeneTonic_2.4.2.tar.gz
Windows Binary	GeneTonic_2.4.2.zip (64-bit only)
macOS Binary (x86_64)	GeneTonic_2.4.2.tgz
macOS Binary (arm64)	GeneTonic_2.4.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeneTonic
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeneTonic
Bioc Package Browser	https://code.bioconductor.org/browse/GeneTonic/
Package Short Url	https://bioconductor.org/packages/GeneTonic/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive