4 questions
0
votes
0
answers
12
views
Zarr: KeyError .zarray when opening anndata group
When I try to open an anndata group object with zarr using a store:
group = zarr.group(store=self._store)
I get a keyError on .zarray. zarr is trying to figure out if certain folders are arrays or ...
- 2,384
-1
votes
0
answers
19
views
BracketError when using diffxpy for a scRNAseq experiment
I am trying to use diffxpy to do differential gene expression analysis between 2 samples (batch) in one cell type from a scRNAseq experiment and I am using the following code:
#subsetting an adata ...
0
votes
0
answers
61
views
Scanpy Neighborhood Graph Construction Error: "'NoneType' object has no attribute 'split'"
I am running a standard scanpy workflow on a dataset and I reached the neighborhood graph construction.
When I run the line:
sc.pp.neighbors(adata, n_neighbors=10, n_pcs=11)
I get the following error:
...
- 1
2
votes
1
answer
56
views
How to plot anndata like matrix to grey 2d numpy array
Input data
mtx: "<COOrdinate sparse matrix of dtype 'int64' with 357558594 stored elements and shape (30562, 96629557)>"
mtx.todense()[0:2,0:8] = matrix([[4050, 24, 21, 3, ...
- 2,012