├── .gitignore ├── CHANGES.md ├── LICENSE ├── README.md ├── images └── monet_logo_25perc.jpg ├── monet ├── __init__.py ├── batch_correct │ ├── __init__.py │ └── mnn.py ├── cluster │ ├── __init__.py │ ├── density.py │ ├── diff_exp.py │ ├── graph.py │ ├── hierarchical.py │ └── util.py ├── core │ ├── __init__.py │ ├── exp_matrix.py │ └── exp_profile.py ├── data │ ├── RdBu_r_colormap.tsv │ ├── gene_lists │ │ ├── mitochondrial_human.txt │ │ ├── mitochondrial_mouse.txt │ │ ├── mitochondrial_zebrafish.txt │ │ ├── mt_ribosomal_human.txt │ │ ├── ribosomal_human.txt │ │ ├── ribosomal_mouse.txt │ │ └── ribosomal_zebrafish.txt │ └── test │ │ ├── pbmc_100_compressed_data.pickle │ │ ├── pbmc_100_decompressed_expression.npz │ │ ├── pbmc_100_denoised_expression.npz │ │ ├── pbmc_100_expression.npz │ │ ├── pbmc_100_expression.tsv │ │ ├── pbmc_100_pc1_restored_expression.npz │ │ ├── pbmc_100_pc1_scores.tsv │ │ ├── pbmc_100_pca_model.pickle │ │ ├── pbmc_1k_expression.npz │ │ └── pbmc_1k_v3_filtered_feature_bc_matrix.tar.gz ├── denoise │ ├── __init__.py │ ├── cli.py │ ├── enhance_model.py │ ├── mcv.py │ └── util.py ├── enrichment │ ├── __init__.py │ ├── enrichment_model.py │ ├── gene_set.py │ ├── gene_set_collection.py │ ├── result.py │ └── util.py ├── helper │ ├── __init__.py │ └── helper.py ├── label_transfer │ ├── __init__.py │ └── knn.py ├── latent │ ├── __init__.py │ ├── compressed_data.py │ ├── monet_model.py │ ├── pca_model.py │ └── util.py ├── ontology │ ├── __init__.py │ ├── gene_ontology.py │ ├── go_annotation.py │ ├── go_term.py │ └── util.py ├── preprocess │ ├── __init__.py │ ├── preprocess.py │ └── qc.py ├── simulate │ ├── __init__.py │ └── sim_enhance.py ├── util │ ├── __init__.py │ ├── annotations.py │ ├── data.py │ ├── expression.py │ ├── fdr.py │ ├── files.py │ ├── genes.py │ ├── logging.py │ └── sample.py ├── velocyto │ ├── __init__.py │ ├── data.py │ └── util.py ├── visualize │ ├── __init__.py │ ├── cells.py │ ├── force.py │ ├── genes.py │ ├── heatmap.py │ ├── plotly_subtype.py │ ├── tsne.py │ ├── umap.py │ └── util.py └── workflows │ ├── __init__.py │ ├── clustering.py │ ├── denoising.py │ ├── heatmap.py │ ├── nonlinear.py │ ├── preprocess.py │ ├── scvelo.py │ └── util.py ├── setup.py └── tests ├── conftest.py ├── core └── test_exp_matrix.py ├── denoise ├── conftest.py ├── test_cli.py ├── test_compressed_data.py └── test_enhance.py ├── latent └── test_pca_model.py └── pytest.ini /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/monet/HEAD/.gitignore -------------------------------------------------------------------------------- /CHANGES.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/monet/HEAD/CHANGES.md -------------------------------------------------------------------------------- /LICENSE: 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