├── .gitignore ├── Guide_containerized_vm.rst ├── LICENSE ├── README.md ├── scCloud ├── CODE_OF_CONDUCT.md ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── docs │ ├── Makefile │ ├── _static │ │ └── css │ │ │ └── custom.css │ ├── api │ │ └── index.rst │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── references.rst │ ├── release_notes.rst │ ├── requirements.txt │ └── usage.rst ├── scCloud │ ├── __init__.py │ ├── __main__.py │ ├── annotate_cluster │ │ ├── __init__.py │ │ ├── annotate_cluster.py │ │ ├── human_brain_cell_markers.json │ │ ├── human_immune_cell_markers.json │ │ ├── mouse_brain_cell_markers.json │ │ ├── mouse_immune_cell_markers.json │ │ └── run_annotate_cluster.py │ ├── check_sample_indexes │ │ ├── __init__.py │ │ ├── check_sample_indexes.py │ │ └── chromium-dna-sample-indexes-plate.json │ ├── cite_seq │ │ ├── __init__.py │ │ └── cite_seq.py │ ├── commands │ │ ├── AggregateMatrix.py │ │ ├── AnnotateCluster.py │ │ ├── Base.py │ │ ├── CITESeq.py │ │ ├── CheckSampleIndexes.py │ │ ├── Clustering.py │ │ ├── DeAnalysis.py │ │ ├── DemuxEM.py │ │ ├── DownSample.py │ │ ├── FindMarkers.py │ │ ├── PARQUET.py │ │ ├── Plotting.py │ │ ├── SCPOutput.py │ │ ├── SubClustering.py │ │ ├── View.py │ │ ├── __init__.py │ │ └── iPlotting.py │ ├── demuxEM │ │ ├── __init__.py │ │ ├── demuxEM.py │ │ ├── down_sampling.py │ │ └── plot.py │ ├── ext │ │ ├── forceatlas2.jar │ │ └── gephi-toolkit-0.9.2-all.jar │ ├── misc │ │ ├── __init__.py │ │ └── misc.py │ ├── pipeline │ │ ├── __init__.py │ │ ├── cite_seq.py │ │ ├── demuxEM_pipeline.py │ │ └── pipeline.py │ ├── plotting │ │ ├── __init__.py │ │ ├── iplot_library.py │ │ ├── plot_library.py │ │ ├── plot_qc.py │ │ ├── plot_utils.py │ │ └── run_plotting.py │ └── tools │ │ ├── __init__.py │ │ ├── batch_correction.py │ │ ├── clustering.py │ │ ├── convert_to_parquet.py │ │ ├── de_analysis.py │ │ ├── diffusion_map.py │ │ ├── down_sampling.py │ │ ├── gradient_boosting.py │ │ ├── graph_operations.py │ │ ├── hvg_selection.py │ │ ├── logging.py │ │ ├── manage_10x_h5_matrices.py │ │ ├── nearest_neighbors.py │ │ ├── net_regressor.py │ │ ├── preprocessing.py │ │ ├── readwrite.py │ │ ├── remove_ambient.py │ │ ├── scp_output.py │ │ ├── subcluster_utils.py │ │ └── visualization.py ├── setup.cfg └── setup.py └── tests ├── data ├── aggregate_multi_genome.csv ├── aggregate_test.csv ├── heart_1k_v2 │ └── filtered_gene_bc_matrices_h5.h5 ├── heart_1k_v3 │ └── filtered_gene_bc_matrices_h5.h5 └── pbmc_1k_protein_v3 │ └── filtered_gene_bc_matrices_h5.h5 ├── test_aggregate.py └── test_pipeline.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/broadinstitute/scRNA-Seq/HEAD/.gitignore -------------------------------------------------------------------------------- /Guide_containerized_vm.rst: -------------------------------------------------------------------------------- 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