GeneTonic

This package is for version 3.20 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: 3.20

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] ORCID iD ORCID: 0000-0003-3252-7758 , Annekathrin Ludt [aut] ORCID iD ORCID: 0000-0002-2475-4945

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

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

Installation

To install this package, start R (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DifferentialExpression, GO, GUI, GeneExpression, GeneSetEnrichment, Pathways, ReportWriting, ShinyApps, Software, Transcription, Transcriptomics, Visualization

Version 3.0.0

In Bioconductor since BioC 3.11 (R-4.0) (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 (>= 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

System Requirements

URL https://github.com/federicomarini/GeneTonic

Bug Reports https://github.com/federicomarini/GeneTonic/issues

Suggests knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0)

Linking To

Enhances

Depends On Me

Imports Me GeDi

Suggests Me mosdef

Links To Me

Build Report Build Report

Package Archives

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

Source Package GeneTonic_3.0.0.tar.gz

Windows Binary (x86_64) GeneTonic_3.0.0.zip

macOS Binary (x86_64) GeneTonic_3.0.0.tgz

macOS Binary (arm64) GeneTonic_3.0.0.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