API Reference

Modules

• harmonypy_gpu
• kernels
• pp
• trim_merge_marker
• util

Classes

• harmonypy_gpu.Harmony
• pp.ScaleSC: ScaleSC integrated pipeline in a scanpy-like style.
• trim_merge_marker.UF
• trim_merge_marker.data2UF
• util.AnnDataBatchReader: Chunked dataloader for extremely large single-cell dataset. Return a data chunk each time for further processing.

Functions

• harmonypy_gpu.get_dummies: Return a sparse dummy matrix.
• harmonypy_gpu.get_usage
• harmonypy_gpu.moe_correct_ridge
• harmonypy_gpu.run_harmony: Run Harmony.
• harmonypy_gpu.safe_entropy
• harmonypy_gpu.to_csc_cuda: Move to GPU as a csc_matrix, speed up column slice.
• harmonypy_gpu.to_csr_cuda: Move to GPU as a csr_matrix.
• kernels.get_find_indices
• kernels.get_mean_var_major
• kernels.get_mean_var_minor
• trim_merge_marker.X_to_GPU: Transfers matrices and arrays to the GPU.
• trim_merge_marker.adata_cluster_merge: Need a description.
• trim_merge_marker.wrapper
• trim_merge_marker.wrapper
• trim_merge_marker.wrapper
• trim_merge_marker.find_cluster_pairs_to_merge
• trim_merge_marker.find_markers
• trim_merge_marker.fraction_cells: Given adata.X (n cells * m genes), ctype_col (a column name in adata.obs that stores the cell type annotation), and a glist (for example, [gene1, gene2, ..., genek])
• trim_merge_marker.marker_filter_sort
• trim_merge_marker.wrapper
• trim_merge_marker.myNSForest
• trim_merge_marker.wrapper
• trim_merge_marker.wrapper
• trim_merge_marker.wrapper
• trim_merge_marker.specificity_score
• trim_merge_marker.stds: Variance of sparse matrix a
• trim_merge_marker.timer
• util.check_dtype: Convert dtype to float32 or float64.
• util.check_nonnegative_integers: Check if X is a nonnegative integer matrix.
• util.correct_leiden
• util.csr_col_index
• util.csr_indptr_to_coo_rows
• util.csr_row_index: Populate indices and data arrays from the given row index.
• util.filter_cells: Cell filtering according to min and max gene counts.
• util.find_indices
• util.gc: Release CPU and GPU RAM
• util.get_mean_var: Calculating mean and variance of a given matrix based on customized kernels.
• util.harmony: Harmony GPU version.
• util.svd_flip: Flip the signs of loading according to sign(max(abs(loadings))).
• util.write_to_disk

---

This file was automatically generated via lazydocs.