joseph-siefert

scGen model is very slow

9

Thanks for the great tools! Is the scGen model in scArches using the newest scGen version? I can run scGen no problem and it runs pretty fast, but when I...

segfault when converting h5ad to SCE

3

Thanks for the great tool. Unfortunately I am getting a segmentation error when converting a large dataset. A smaller subset works without issue. Here is the error from the large...

OutOfMemoryError when running run_tensor_cell2cell_pipeline on GPU

3

The memory at each iteration seems to accumulate. Is it possible to release it or chuck it differently to circumvent this issue? ``` Running Elbow Analysis 24%|██▍ | 6/25 [23:50...

Error querying biomart

3

Both of the following code blocks give similar errors: ``` from pybiomart import Server server = Server(host='http://www.ensembl.org') dataset = (server.marts['ENSEMBL_MART_ENSEMBL'] .datasets['hsapiens_gene_ensembl']) dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'], filters={'chromosome_name': ['1','2']}) Traceback (most recent call last):...

Error moving adata.X to GPU

13

**Describe the bug** When running either command `adata.X = cpx.scipy.sparse.csr_matrix(adata.X)` or `rsc.get.anndata_to_GPU(adata)`, I get the following error: ``` --------------------------------------------------------------------------- TypeError Traceback (most recent call last) File :1 File [/mambaforge/envs/rapids_singlecell_24.06/lib/python3.11/site-packages/cupyx/scipy/sparse/_compressed.py:228](http://nruslj-cph510003:8888/mambaforge/envs/rapids_singlecell_24.06/lib/python3.11/site-packages/cupyx/scipy/sparse/_compressed.py#line=227), in...