This repository contains the notebooks used to analyze tomo-seq data of human gastruloids, and to perfom the comparison with mouse gastruloids. Notebooks are organized as:
1 - Pre-processing of raw data: selection of tomo-seq sections with gastruloid material, normalization of the data, and filtering of suspicious genes.
2 - Gene reproducibility: Gene reproducibility between gastruloid replicates is evaluated.
3 - Plots: heatmaps, gene expression profiles for hox and germ-layer related genes are performed, and heatmaps with scaled z-scores.
4 - Comparison between human and mouse gastruloids, and GO terms analysis using the python goatools package.