The goal of GeneTonic is to analyze and integrate the results from Differential Expression analysis and functional enrichment analysis.
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.
GeneTonic can be found on Bioconductor (https://www.bioconductor.org/packages/GeneTonic).
A preprint :page_facing_up: on GeneTonic is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1.
You can install the development version of GeneTonic from GitHub with:
This is a basic example which shows you how to use
GeneTonic on a demo dataset (the one included in the
library("GeneTonic") example("GeneTonic") # which will in the end run library("macrophage") library("DESeq2") library("org.Hs.eg.db") library("AnnotationDbi") # dds object data("gse", package = "macrophage") dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) dds_macrophage <- estimateSizeFactors(dds_macrophage) # annotation object anno_df <- data.frame( gene_id = rownames(dds_macrophage), gene_name = mapIds(org.Hs.eg.db, keys = rownames(dds_macrophage), column = "SYMBOL", keytype = "ENSEMBL"), stringsAsFactors = FALSE, row.names = rownames(dds_macrophage) ) # res object data(res_de_macrophage, package = "GeneTonic") res_de <- res_macrophage_IFNg_vs_naive # res_enrich object data(res_enrich_macrophage, package = "GeneTonic") res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) GeneTonic(dds = dds_macrophage, res_de = res_de, res_enrich = res_enrich, annotation_obj = anno_df, project_id = "my_first_genetonic")
You can find the rendered version of the documentation of
GeneTonic at the project website https://federicomarini.github.io/GeneTonic, created with
Please visit http://shiny.imbei.uni-mainz.de:3838/GeneTonic/ to see a small demo instance running, on the
If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an issue.
Please note that the
GeneTonic project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
MIT © Federico Marini