Code of the analysis for the Sciacovelli_Dugourd_2021 manuscript.
Scripts are located in the scripts folder.
In order to run them, simply open Sciacovelli_Dugourd_2021_paper.Rproj in R studio.
You will need to instal the following packages:
From bioconductor (release 3.14 or higher): GSEABase; biomaRt; clusterProfiler; dorothea; fgsea ;limma; viper; vsn
From Cran: cowplot (>=1.1.1); dplyr (>=1.0.9); ggfortify (>=0.4.14); ggplot2 (>=3.3.6); ggrepel (>=0.9.1); gridExtra (>=2.3);igraph (>=1.3.1); pheatmap (>=1.0.12); readr (>=2.1.2); readxl (>=1.4.0); reshape2 (>=1.4.4); visNetwork (>=2.1.0)
From github (latest version): decoupleR (https://github.com/saezlab/decoupleR) ; ocean (https://github.com/saezlab/ocean)
Enjoy !
Citing code:
