Closed demar01 closed 2 years ago
Hey! We ran scran normalization on the data to normalize it and put the data that was initially in adata.X
in adata.layers['counts']
. The function for that should just be scib.pp.normalize()
from the scib package here. That should generate exactly the version of the simulation data you need. Maybe @lazappi can confirm this.
Hey @demar01 @lazappi just highlighted the simulation datasets were not on figshare, so I added them. You can find them here.
Thanks so much!!
Hello, First of all, thank you for this fantastic package!
When I generate the simulated data sim1 from here that Anndata does not contain a 'counts' layer in 'adata.layers[
counts
]', and therefore I cannot use it for the integration partWould it be possible to get the steps to generate the dataset used in the integration part, '/storage/groups/ml01/workspace/scIB/simulations_1_1/sim1_1_norm.h5ad'? Also that data should not be normalized, but the name is sim1_1_norm.h5ad?
Many thanks!