This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GeneTonic.
Bioconductor version: 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")
):
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.
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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) (0.5 years) |
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 |
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 |
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