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+# The repository for our work on breast cancer neoadjuvant treatment (preprint).
+
+This repository contains all the scripts required to reproduce our analysis, along with all necessary local files. It also contains the output files that are produced (plots, spreadsheets etc.).
+
+### **The R scripts are all under the folder** `R_Scripts`. 
+- `Preprocessing_and_QC.R` contains the code for downloading the gene expression studies, the preprocessing of the data and the production of diagnostic plots and exploratory analysis plots. 
+- `DGEA_ML_Networks.R` contains the code for the downstream analysis: Differential Gene Expression Analysis, Machine Learning methods (unsupervised and supervised), model evaluation and the use of the `pathfindR` package to conduct Active Subnetwork Enrichment analysis. 
+- `Signatures.R` contains the code that was used to compare our signature (NAT Response signatures, *NRS*) to previously published breast cancer signatures and immune signatures.
+- `Exploratory_barcharts.R` contains the code for producing exploratory plots from our data.
+
+Two additional scripts are included: 
+- `Genefu_functions.R` defines the functions required for our `genefu` annotation pipeline.
+
+The session info files in the `R_Scripts` folder report the versions of the packages that were used when the final results were produced.
+
+Even if it seems like 99% of the code in this repository is **HTML**, it is really purely **R**, but the vast majority of the output plots are .html files.
+
+## Important:
+Not all data are yet available in the repository. Permission for response data from one study is pending.