Dynamic expression of CD9 protein in T-cell acute lymphoblastic leukemia : Bioinformatics resources and Docker environments

This repository provides Docker containers designed to reproduce the analyses presented in Quessada, Nozais et al. (2026), along with selected intermediate files. Detailed instructions for reproducing the analysis are available on github (https://github.com/JulienRey1/CD9/). for bulkRNA, raw data (FASTQ files), as well as intermediate count tables for all samples, are available in GEO (GSE319183). This Zenodo hosts the following resources : Docker images used for the analysis (seurat500.tar and rna_analysis.tar) Preprocessed single-cell RNA-seq data (sickphys_reg.Robj) Raw counts for single-cell RNA-seq (counts.txt) Normalized counts for single-cell RNA-seq (counts_norm.txt) Preprocessed bulk RNA-seq data (edgeR_fit.rds) Filtered and annotated bulkRNA-seq count data (data.filtered.rds) Flow cytometry data measuring CD9 expression in PDX #11 and PDX #65