GeneTonic

DOI: 10.18129/B9.bioc.GeneTonic    

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

Bioconductor version: Release (3.11)

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 (!requireNamespace("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, Software, Transcription, Transcriptomics, Visualization
Version 1.0.1
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports AnnotationDbi, bs4Dash, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, 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
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_1.0.1.tar.gz
Windows Binary GeneTonic_1.0.1.zip
macOS 10.13 (High Sierra) GeneTonic_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneTonic
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneTonic
Package Short Url https://bioconductor.org/packages/GeneTonic/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: