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Cell cycle genes #10

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Lila3141 opened this issue Dec 12, 2022 · 0 comments
Open

Cell cycle genes #10

Lila3141 opened this issue Dec 12, 2022 · 0 comments

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@Lila3141
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Hi,

I noticed that there are some cell cycle genes in the hvgs of your final objects, namely
"FAM111B" "HELLS" "HMMR" "RTKN2" "MNS1" "RIBC2" "TMPRSS11B" "WDR54" "CCDC34" "MYEF2"
cell cycle genes: https://github.com/TheJacksonLaboratory/endometriosis-scrnaseq/blob/main/databases/cell_cycle.csv
Final objects: https://singlecell.jax.org/datasets/endometriosis-2022 .h5ad objects; @assays[["RNA"]]@meta.features[["highly_variable"]]

In the methods section of the paper it says that all cell cycle genes were excluded from the hvg list. Is there a reason why you keep these 10 genes?
Thank you in advance

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