Guidelines to Manipulate Clinical Data

Contact:

• rlink@cea.fr

Authors:

• celine.bourdon@inserm.fr
• dimitri.papadopoulos@cea.fr
• edouard.duches@cea.fr

Content

documents/
├── dataset-clinical_version-2_description.pdf: Annotated eCRF
├── dataset-clinical_version-2_description_file-information.xlsx: Variable description and mapping to file
├── rlink_webinar_clinical-data_manipulation.pdf: Presentation
└── sop_eCRF.docx: Standard Operating Procedures (Detailed information)

python/
├── pixi.toml: Config file for python 
├── usecase1_extract_demographicSmokingLithemiaMarsResponse.py: use case in python
└── utils_build_description_file.py

R/
├── usecase1_extract_demographicSmokingLithemiaMarsResponse_classic.R: use case in classic R
└── usecase1_extract_demographicSmokingLithemiaMarsResponse_tidyverse.R: use case in R with tidyverse

Running Python code

1. Install Pixi

   Linux & macOS

   curl -fsSL https://pixi.sh/install.sh | bash
   

   Windows

   iwr -useb https://pixi.sh/install.ps1 | iex
   

2. Go to the Python directory, then install the required Python packages (only the first time):

cd python
pixi install

3. Set up Python configuration:

cd python
pixi shell

Running R code

Install RStudio