Comments (3)
Sorry for the delayed response. The h5 files can be found at https://cblast.gao-lab.org/download. You can click the dataset names (first column) there to download the h5 files.
from cell_blast.
Thanks for your response and it is helpful. However, what I want to know is that how should I creat "h5" files that satisfy the input of Cell_BLAST with my own data which your datasets didn't contain.
from cell_blast.
In that case, it might be unnecessary to convert to the h5 files and load them from disk. What's the current data format you have? If it's in AnnData or Loom format, you can use the from_anndata
or from_loom
methods to convert them into cb.data.ExprDataSet
class, which can then be used as input of Cell BLAST. Otherwise, you may first manually read your dataset into memory, and then create a cb.data.ExprDataSet
object (via the class constructor) with the expression matrix, cell meta table and gene meta table. To save the cb.data.ExprDataSet
object to h5 files, use the write_dataset
method.
Hope that helps!
from cell_blast.
Related Issues (20)
- Web ERROR while uploading loom/h5ad: 'dict' object has no attribute 'dtype' HOT 3
- reconcile_models() problems HOT 14
- how to read the dataset file HOT 2
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- How to use gpu to accelerate train? HOT 3
- KeyError: "Unable to open object (object 'obs' doesn't exist)" HOT 1
- how to use HOT 5
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- Cross-Species Celltype Annotation HOT 5
- The website cblast.gao-lab.org is unreachable. The connection was unexpectedly terminated. HOT 4
- Update the reference dataset. HOT 1
- Error in "cb.directi.fit_DIRECTi()" function
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