GhostInTheShellwjc

1. A function can be added to convert counts to formats such as TPM according to species, with automatic determination of gene formats, similar to the "count2tpm" function in the...

1.An Api doc for many of main func is required. 2.In ov.pp.qc,can we identify the mitochondrion genes automatically? Sometimes,we may forget to change the MT_startwith when we process statistic from...

1.scVI enables model hyperparameter tuning by scVI.autotune.I think it is awesome if we can have the feature in functions which use scVI,or it can be added into deep learning methods...

I encounter the same problem with you.It only influences the left part of the picture,and the umap picture is right.You can draw a pie chart instead of the left part...

I'm very sorry for the confusion my information has caused you. I can provide some more detailed information. In the omicverse tutorial "Different Expression Analysis with DEseq2," the gsea_obj.plot_enrichment function...

@HendricksJudy If possible, could you please also take a look at issues #216 and #218? Thank you very much. BTW, when running deep learning algorithms on Jupyter in VSCode, it...

Pandas==1.5.3 can solve

Perhaps you can modify your numpy version to 1.26.4 and have a try.It goes well on my Jupyter on vscode in Windows 11. If you need version info about other...

@CarrieChen0530 python 3.10.15 pydeseq2 0.4.12 pandas 1.5.3？follow your codes in the first time

Downgrading your gseapy to 0.10.8 may help.However，I really hope if the newest gseapy would join in the next version of omicverse.