import scaled data

[java0485]

Hello,

I use the ScaleData function of Seurat to remove cell cycle effects. Can you comment on how to import/load these data to either the web-based or local version of spring?
If I may, the best case scenario will involved transformation/export of the seurat object as this contains all relevant metadata, filtering, normalization and scaling data.

Thanks in advance,

Jose

[calebweinreb]

Hi, The easiest way to automatically convert your whole Seurat object to SPRING would be via scanpy. I believe it is possible to convert from Seurat to scanpy (see here) <https://satijalab.org/seurat/conversion_vignette.html>, and then scanpy has a method <https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export> to generate a SPRING plot. You could also do this manually. Have you looked at this tutorial <https://github.com/AllonKleinLab/SPRING_dev/blob/master/data_prep/spring_example_pbmc4k.ipynb>for making a SPRING plot? To use it, you would just need to export the relevant data from Seurat into python somehow and go from there.

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On Tue, Feb 12, 2019 at 6:01 PM java0485 ***@***.***> wrote: Hello, I use the ScaleData function of Seurat to remove cell cycle effects. Can you comment on how to import/load these data to either the web-based or local version of spring? If I may, the best case scenario will involved transformation/export of the seurat object as this contains all relevant metadata, filtering, normalization and scaling data. Thanks in advance, Jose — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF3OspS1Sh-nFowHy16bCCi7oapKGrMrks5vM0fTgaJpZM4a4O4Y> .

[liuweihanty]

hi @calebweinreb, just a follow up regarding the turorial you mentioned to export Seurat to python and do spring plot manually:https://github.com/AllonKleinLab/SPRING_dev/blob/master/data_prep/spring_example_pbmc4k.ipynb

This page is no longer there, is there an updated turtorial somewhere? Thanks!

[calebweinreb]

What do you see when you open the link? I tested on a few computers and saw the notebook.

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On Wed, Apr 28, 2021 at 5:46 PM liuweihanty ***@***.***> wrote: hi @calebweinreb <https://github.com/calebweinreb>, just a follow up regarding the turorial you mentioned to export Seurat to python and do spring plot manually: https://github.com/AllonKleinLab/SPRING_dev/blob/master/data_prep/spring_example_pbmc4k.ipynb This page is no longer there, is there an updated turtorial somewhere? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MUDQXCE6QD5NIDXCKLTLB64HANCNFSM4GXA5YMA> .

[liuweihanty]

Hi @calebweinreb it is normal on my end as well now! It was 404 page not found (sth like that) the other day.