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README.Rmd
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README.Rmd
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---
output: github_document
---
<img src="man/figures/GeneTonic.png" align="right" alt="" width="120" />
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# GeneTonic
<a href="https://doi.org/10.1186/s12859-021-04461-5"><img src="https://img.shields.io/badge/doi-GeneTonic-blue.svg"><a>
<a href="https://doi.org/10.1002/cpz1.411"><img src="https://img.shields.io/badge/doi-GeneTonic_protocol-blue.svg"><a>
<!-- badges: start -->
[](https://github.com/federicomarini/GeneTonic/actions)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/GeneTonic/)
[](https://github.com/federicomarini/GeneTonic/commits/master)
[](https://www.tidyverse.org/lifecycle/#stable)
[](https://codecov.io/github/federicomarini/GeneTonic)
<!-- badges: end -->
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).
If you use GeneTonic in your work, please refer to the original publication :page_facing_up: on BMC Bioinformatics (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5, doi: [10.1186/s12859-021-04461-5](https://doi.org/10.1186/s12859-021-04461-5)).
A preprint :page_facing_up: on GeneTonic is available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1.
## Installation
You can install the development version of GeneTonic from GitHub with:
```{r eval=FALSE}
library("remotes")
remotes::install_github("federicomarini/GeneTonic",
dependencies = TRUE, build_vignettes = TRUE)
```
## Example
This is a basic example which shows you how to use `GeneTonic` on a demo dataset (the one included in the `macrophage` package).
```{r eval=FALSE}
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")
```
## Usage overview
You can find the rendered version of the documentation of `GeneTonic` at the project website https://federicomarini.github.io/GeneTonic, created with `pkgdown`.
## Sneak peek?
Please visit http://shiny.imbei.uni-mainz.de:3838/GeneTonic/ to see a small demo instance running, on the `macrophage` dataset.
## Development
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](https://github.com/federicomarini/GeneTonic/issues).
## Code of Conduct
Please note that the GeneTonic project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
## License
MIT © Federico Marini