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dpeerlab / Palantir

Single cell trajectory detection
https://palantir.readthedocs.io
GNU General Public License v2.0
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Is it possible to run palantir on batch corrected data? #104

Closed jesswhitts closed 1 year ago

jesswhitts commented 1 year ago

Hello,

I was just wondering if it is possible to run this on batch corrected data? SCVI corrected to be more specific. The counts themselves are not actually altered, but "X_scVI" is used as input for dimensionality reduction rather than using PCs. So could I run this and just use "X_scVI" rather than "X_pca"?

Many thanks, Jess

ManuSetty commented 1 year ago

Yes - you should be able to use X_scVI as input to computing diffusion components

On Mon, May 22, 2023 at 03:50 jesswhitts @.***> wrote:

Hello,

I was just wondering if it is possible to run this on batch corrected data? SCVI corrected to be more specific. The counts themselves are not actually altered, but "X_scVI" is used as input for dimensionality reduction rather than using PCs. So could I run this and just use "X_scVI" rather than "X_pca"?

Many thanks, Jess

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jesswhitts commented 1 year ago

It works. Thanks! :)