README.md

Code and Data accompanying Molecular International Prognostic Scoring System for Myelodysplastic Syndromes

Bernard E, Tuechler H, Greenberg PL, Hasserjian RP, Arango Ossa JE et al. NEJM Evidence 2022.

📂 Repository Structure

• data/: the folder contains the clinical and molecular data necessary to reproduce the results of the study. See the README in the data/ folder for details about data structure.

• IPSSM.ipynb: the jupyter notebook with R code to reproduce results and figures.

• IPSSM.html: an html version of the notebook.

• bed/: the target bed file (hg19) used for NGS capture in the study.

🚀 Getting started with this repository

Clone the repository

To clone this repository on your local computer please run:

$ git clone https://github.com/papaemmelab/IPSSMstudy

R packages you need to install:

# run in an R console
install.packages('ggplot2',      repos = 'http://cran.us.r-project.org')
install.packages('survival',     repos = 'http://cran.us.r-project.org')
install.packages('survminer',    repos = 'http://cran.us.r-project.org')
install.packages('cmprsk',       repos = 'http://cran.us.r-project.org')
install.packages('cowplot',      repos = 'http://cran.us.r-project.org')
install.packages('dplyr',        repos = 'http://cran.us.r-project.org')
install.packages('tidyr',        repos = 'http://cran.us.r-project.org')
install.packages('ggsci',        repos = 'http://cran.us.r-project.org')
install.packages('ggpubr',       repos = 'http://cran.us.r-project.org')
install.packages('RColorBrewer', repos = 'http://cran.us.r-project.org')
install.packages('MetBrewer',    repos = 'http://cran.us.r-project.org')

# install the IPSS-M R package
install.packages('devtools', repos = 'http://cran.us.r-project.org')
library(devtools)
install_github("papaemmelab/ipssm", ref="master")

❓ Question

If any question on the repo, feel free to contact Elsa.