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# Shiny SChnurR
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<img src="https://zupimages.net/up/19/18/zpld.png" alt="Logo"
	title="SChnurR logo" width="42" height="42" /> **Direct Link of the Tool :** https://shiny-bird.univ-nantes.fr/jbalberge/schnurr/
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## Introduction
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Shiny SChnurR is a visualisation tool for single-cell RNA-seq analysis developped in R Shiny.

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## Installation
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To use Shiny SChnurR, you first need to :
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1. Install [R][R], version 3.6 (Planting of a Tree) or greater.
2. Install some packages with the script **install.R** (*cf Required Packages part* ).
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3. Download all files of this project, or clone it.
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Then, you simply need to launch R and this command :
```r
shiny::runApp('/my/path/to/my/folder/which/contain/all/the/files')
```

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The .rds files used must have been made with the analysis pipeline available at this adress : 
https://gitlab.univ-nantes.fr/E176261N/singlecell
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## Conda install

To install SChnurR in a conda environment, run the following commands:

```
conda create -n schnurr -c conda-forge -c bioconda r=3.5 \
    r-shiny r-shinythemes r-seurat r-viridis r-shinyjs r-plotly \
    r-shinydashboard r-stringr r-dt r-rcolorbrewer r-data.table \
    r-biocmanager bioconductor-mast bioconductor-org.hs.eg.db   \
    bioconductor-panther.db bioconductor-topgo 
# TODO add clusterprofiler
```

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## Required Packages

Here the list of the required packages for Shiny SChnurR :

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* [Shiny][Shiny]
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* [Seurat][Seurat]
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* shinythemes
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* dplyr
* ggplot2
* viridis
* shinyjs
* stringr
* plotly
* BiocManager
* shinydashboard
* shinyjs
* DT
* RColorBrewer
* MAST
* data.table
* clusterProfiler
* org.Hs.eg.db
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* tools
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* PANTHER.db
* topGO
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* ggpubr
* colourpicker
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All of this packages are installed with the provided script **install.R** and are up-to-date.
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## Tutorial
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Please refer to the Wiki to find some help about using the app.
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## About
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** Shiny SChnurR **
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Centre de Recherche en Cancérologie et Immunologie Nantes-Angers
UMR1232, CNRS ERL6001
IRS-UN - 8 Quai Moncousu - 44007 Nantes

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**Equipe 11** - Oncogénomique intégrative de la genèse et de la progression du Myélome Multiple
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*Mathias Bagueneau, Jean-Baptiste Alberge, Jonathan Cruard*
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----
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[R]: https://www.r-project.org/ "R"
[Seurat]: http://https://satijalab.org/seurat/install.html "Seurat"
[sctransform]: https://rawgit.com/ChristophH/sctransform/master/inst/doc/seurat.html "sctransform"
[Link of the tool]: https://shiny-bird.univ-nantes.fr/jbalberge/schnurr/ "Link of the tool"
[shiny]: https://shiny.rstudio.com/ "shiny"