This repository contains markdown scripts for the RA-Map project.
In the EDA directory, you'll find markdown documents summarizing our outlier detection and removal procedures for transcriptomic data at baseline ("0m_outliers.md") and 6-months ("6m_outliers.md"). You'll also find EDA pipelines for all platforms, including RDS data objects for autoantibody, metabolomics (serum and urine), miRNA, and proteomics. RDS data objects for mRNA are located in figshare (https://figshare.com/projects/RA-Map_a_multi-omic_immune_cell_landscape_in_early_RA/76398)
The "Imputing_clinical.md" file describes our procedure for imputing gender and height.
The "DEA.md" file summarizes our differential expression analyses for transcriptomic data, testing for associations with disease and response.
UPSETR figure summarising overlap between multi-omic samples in the TACERA cohort
