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rajewsky-lab / novosparc

BSD 3-Clause "New" or "Revised" License
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Different grids shapes and spatially informative genes #11

Closed arielmadr closed 4 years ago

arielmadr commented 4 years ago

Hi,

Thank you for the fantastic package. I've used the reconstruct_tissue.py script with my data and the results look promising. However, I have a couple of questions:

1) I was wondering, do you have any suggestions in how to use different shapes for the grids ( like circles or elipses)? 2) Do you have any function in the package to use for identify spatially informative genes? I couldn't find it.

Thanks a lot!

Ariel

nukappa commented 4 years ago

Hi, thanks for your feedback, much appreciated!

  1. I just pushed version 0.3.9 which contains a function that can be used for custom target spaces, see also the docs for more details.
  2. This is still in the pipeline, shouldn't take longer to appear.

Nikos

enessenel commented 4 years ago

Algorithm to identify spatially informative genes is implemented now in 7bf55f986ca1ef213a89c04813969a38c30ad2b5 and available with the version 0.3.10.