Add files and update Readme

README.md

 # TDD Project
+
+This repository contains all `R` scripts, and example files, permitting to
+generate `Random Forest` models to predict `Translation Independent Degradation`
+and `Translation Dependent Degradation`.
+
+This repository has been build on `Ubuntu 20.04` and validated on the most
+recent versions of `R (4.3.2 2023-10-31 -- "Eye Holes")` and
+`RStudio 2023.09.1 Build 494`.
+
+A `Shiny` powered Rmarckdown file is provided to facilitate the generation of
+of `Random Forest` models.
+
+For all information or problem concerning this repository please contact:
+david.cluet@ens-lyon.fr
+
+Our complete processed database and additional filter files are available 
+as a 25MB file (`RMI2_tdd_project_databases.zip`) upon request:
+emiliano.ricci@ens-lyon.fr
+
+
+## Degradation Indexes
+
+Our reference degradation indexes are computed for the **3h** time point
+as follow using **normalized count reads**.
+
+Absolute $Degradation Fold = {1 - {counts(t3h, Trip) \over counts(t0,Trip)}}$
+
+Absolute $TID_{index} = {{counts(t0, Trip) - counts(t3h, TripCHX)} \over counts(t0, Trip)}$
+
+Absolute $TDD_{index} = {{counts(t3h, TripCHX) - counts(t3h,Trip)} \over counts(t0, Trip)}$
+
+## Current status of the repository
+
+> - Scripts classification: *In progress*
+> - README and WIKI redaction: *In progress*
+
+## Installation
+
+### Repository
+
+Clone this repository (in your home folder by default).
+
+```bash
+cd ~/
+git clone git@gitbio.ens-lyon.fr:LBMC/RMI2/tdd_project.git
+```
+
+### Dependencies
+
+On `Ubuntu 20.04` some libraries has to be installed on your system before
+installing `R packages`.
+
+To install them execute:
+
+```bash
+sudo apt update
+sudo apt -y upgrade
+sudo apt -y install libcurl4-openssl-dev
+sudo apt -y install libxml2-dev
+sudo apt -y install libssl-dev
+sudo add-apt-repository -y ppa:cran/poppler
+sudo apt-get update
+sudo apt-get install -y libpoppler-cpp-dev
+```
+
+Now the `R packages` can be install with `Rstudio`:
+
+```R
+nstall.packages('rmarkdown', dep = TRUE)
+install.packages('knitr')
+install.packages('tinytex')
+library(tinytex)
+tinytex::install_tinytex()
+install.packages('shiny')
+install.packages('ggplot2')
+install.packages('tidyverse')
+install.packages('randomForest')
+install.packages('caret')
+install.packages('doParallel')
+install.packages('gridExtra')
+install.packages('grid')
+install.packages('SHAPforxgboost')
+```
+
+### Database and filter files
+
+These files are available upon request (david.cluet@ens-lyon.fr or 
+emiliano.ricci@ens-lyon.fr).
+
+- Save the `RMI2_tdd_project_databases.zip` file into the `src/database` folder
+- Extract the files and move them directly into `src/database` folder
+
+The final arborescence should be:
+
+* src
+  * database
+    * 2023-07-17_Subset_Data_processed_Merge.csv
+    * filtred_genes_Lympho_Resting.csv
+    * filtred_genes_Lympho_Activated.csv
\ No newline at end of file

src/database/.gitignore

+*.csv
+*.zip
+