atarashansky / sctransformpy Goto Github PK

File "/data1/fteufel/miniconda_installation/envs/qsc_env/lib/python3.9/site-packages/SCTransform.py", line 104, in SCTransform
    genes_cell_count = X.sum(0).A.flatten()
AttributeError: 'numpy.ndarray' object has no attribute 'A

adata.X = sparse.csr_matrix(adata.X)
SCTransform(adata, inplace=True)

pool.map(_parallel_wrapper, range(umi_bin.shape[1]), chunksize=pc_chunksize)

from SCTransform import SCTransform
import scanpy as sc
import matplotlib.pyplot as plt
import numpy as np
import time

adata = sc.datasets.pbmc3k()
adata_sct = SCTransform(
    adata,
    min_cells=5,
    gmean_eps=1,
    n_genes=2000,
    n_cells=None,  # use all cells
    bin_size=500,
    bw_adjust=3,
    inplace=False,
)