The scRNAseq upstream analysis main steps comprised of cellranger count processing and souporcell (for demultiplexing the samples sequenced together).
Standard QC and filtering steps followed, leading to a midstream aligment/integration of all samples using Seurat (v4). For that each library was SCtransformed, with count number, mitochondrial fraction, S score and G2M score regressed before integrating all samples via CCA. Downstream analyses included annotation transfer using both Azimuth and Symphony, and trajectory analysis using Cellrank (v2) and tradeSeq.



- 00_* : helper wrappers for demultiplexing, alignment and quantification of samples

- 06b_* : script to align all samples using Seurat (v4)

- 07[h|i]* : notebooks for annotation of the integrated/aligned dataset

- 07k4* : notebook for pseudobulk differential expression testing with DESeq2

- 07m* : notebooks and scripts for defining and analysing trajectiories using Cellrank (v2) and tradeSeq

- 07n* : notebook defining Subset1-like cells

- 07o* : notebooks to produce specific figures and table for the manuscript