Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment
The computational analysis and representation of the data single cell mRNA sequencing data to the publication was mainly performed in python.
The code is divided in a preprocessing and a figure plotting Jupyter notebook.
For the screening of cell-cell communications the Unix based software CellphoneDB and R based NicheNet package were used.
The R Markdown files contain the code for dot plot of the CellphoneDB output and for the full NicheNet analysis and plot generation.