pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
2. Error encountered:
<!-- Please specify the **complete** error message (if applicable, otherwise delete this block): -->
```pytb
2024-06-24 11:50:18,063 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.
Traceback (most recent call last):
File "/opt/miniconda3/envs/pyscenic/bin/pyscenic", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/pyscenic/cli/pyscenic.py", line 713, in main
args.func(args)
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/pyscenic/cli/pyscenic.py", line 59, in find_adjacencies_command
ex_mtx = load_exp_matrix(
^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/pyscenic/cli/utils.py", line 134, in load_exp_matrix
return load_exp_matrix_as_loom(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/pyscenic/cli/utils.py", line 82, in load_exp_matrix_as_loom
with lp.connect(fname, mode="r", validate=False) as ds:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/loompy/loompy.py", line 1515, in connect
return LoomConnection(filename, mode, validate=validate)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/loompy/loompy.py", line 98, in __init__
self.attrs = loompy.GlobalAttributeManager(self._file) #: Global attributes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/loompy/global_attribute_manager.py", line 23, in __init__
materialized = loompy.materialize_attr_values(val[()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/loompy/normalize.py", line 91, in materialize_attr_values
if np.issubdtype(a.dtype, np.string_) or np.issubdtype(a.dtype, np.object_):
^^^^^^^^^^
File "/opt/miniconda3/envs/pyscenic/lib/python3.12/site-packages/numpy/__init__.py", line 397, in __getattr__
raise AttributeError(
AttributeError: `np.string_` was removed in the NumPy 2.0 release. Use `np.bytes_` instead.. Did you mean: 'strings'?
Please complete the following information:
pySCENIC version: Single-Cell rEgulatory Network Inference and Clustering (0.12.1+2.geaf23eb)
Installation method: conda
Run environment: bash
OS: mac
Package versions: [obtain using pip freeze, conda list, or skip this if using Docker/Singularity]:
System config: M2 Chip,24 GB RAM,1.5 TB free space.
Describe the bug I am trying to run Pyscenic GRN but its giving me error and i am unable to solve the issue.
Steps to reproduce the behavior
Please complete the following information:
pip freeze
,conda list
, or skip this if using Docker/Singularity]: