5. Differential Expression analysis with [Deseq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) and [edgeR](https://doi.org/10.1093/bioinformatics/btp616).
For Thal vs HD comparison intra population (HSC or MPP - n = 2) we used the simple design with counts ~ condition, whereas for assessing differencies between Thal and HD in HSC and MPP togheter we included the celltype covariate : count ~ celltype + condition. Genes with an FDR < 0.05 or < 0.001 were considered DEGs for intra population comparisons and combined (HSC + MPP) with covariate respectively.
6. Downstream analysis
We performed Over Representation Analyses (ORA) and Gene Set Enrichment Analyses (GSEA) using R/Bioconductor package [clusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html)(v.3.8.1). Pre-ranked gene list according to log2FC was used to perform Gene Set Enrichment Analysis (GSEA). Terms with adjusted p-value (Benjiamini-Hochber correction) less than 0.05 were considered significantly enriched.
