GeneTonic

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GeneTonic.

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


Bioconductor version: 3.12

This package provides a Shiny application that aims to combine at different levels the existing pieces of the transcriptome data and results, in a way that makes it easier to generate insightful observations and hypothesis - 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.

Author: Federico Marini [aut, cre]

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

Citation (from within R, enter citation("GeneTonic")):

Installation

To install this package, start R (version "4.0") 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")
The GeneTonic User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ReportWriting, Software, Transcription, Transcriptomics, Visualization
Version 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports AnnotationDbi, bs4Dash, colorspace, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tools, utils, viridis, visNetwork
System Requirements
URL https://github.com/federicomarini/GeneTonic
Bug Reports https://github.com/federicomarini/GeneTonic/issues
See More
Suggests knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package GeneTonic_1.2.0.tar.gz
Windows Binary GeneTonic_1.2.0.zip
macOS 10.13 (High Sierra) GeneTonic_1.2.0.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 3.12 Source Archive