cell cycle genes

[yueqiw]

Hi,

I'm trying to map velocity vectors onto my existing UMAP/t-SNE embeddings. These embeddings were generated without the effect of cell cycle genes (I tried a few suboptimal ways to do this), so I'd like to filter out cell cycle genes from the Velocyto analysis as well. In the Habel et al notebook, a set of cell cycle genes are downloaded and filtered out:

urlretrieve("http://pklab.med.harvard.edu/velocyto/Haber_et_al/goatools_cellcycle_genes.txt",
            "data/goatools_cellcycle_genes.txt")

How exactly were the cell cycle genes defined in the first place? From the file name, I guess it came from goatools. I would be great if the author could share the script for producing the list of cell cycle genes. Many thanks!

[yueqiw]

I think I might have found the answer:

https://github.com/tanghaibao/goatools/blob/master/notebooks/cell_cycle.ipynb https://github.com/tanghaibao/goatools/blob/master/tests/test_genes_cell_cycle.py