Data used in this project are extracted from Tabula Muris: https://tabula-muris.ds.czbiohub.org/
In particular, the datasets can be found following this link: https://figshare.com/articles/dataset/Single-cell_RNA-seq_data_from_Smart-seq2_sequencing_of_FACS_sorted_cells_v2_/5829687?file=13088129 where Aorta, and Heart sub datasets from FACS.selection have been used and Metadata and Annotations as well.
This project has been conducted by Hugo Hakem as part of Berkeley BIOE249: Computational Functional Genomics taught by the professor Liana Lareau, Department of Bioengineering.
- First, please download the recquired data-sets as explained above.
- Please download the Jupyter Notebook.
- You may want to run in your terminal the following:
pip install scprep
pip install umap-learn
pip install phate
pip install phenograph
pip install tasklogger
pip install harmonypy
pip install pandas
pip install numpy
pip install sklearn
pip install graphtools
pip install matplotlib
pip install scipy
Interpretation are given as you follow the Jupyter Notebook. Further explanations are provided in the Report.