├── .gitignore ├── AUTHORS ├── LICENSE ├── README.rst ├── pylintrc ├── setup.py ├── singlecell ├── __init__.py ├── data │ ├── gene_lists │ │ ├── mitochondrial_human.tsv │ │ ├── mitochondrial_mouse.tsv │ │ ├── mitochondrial_zebrafish.tsv │ │ ├── ribosomal_human.tsv │ │ ├── ribosomal_mouse.tsv │ │ └── ribosomal_zebrafish.tsv │ ├── indrop │ │ ├── config_template.yaml │ │ ├── gel_barcode1_list.txt │ │ ├── gel_barcode2_list.txt │ │ └── pipeline_template.sm │ └── templates │ │ ├── gcloud │ │ └── indrop_pipeline_wrapper.sh │ │ └── star │ │ ├── build_index.sh │ │ └── map_single-end.sh ├── indrop │ ├── __init__.py │ ├── aligned_reads.py │ ├── barcodes.py │ ├── barcodes_cython.pyx │ ├── cli │ │ ├── __init__.py │ │ ├── check_pipeline.py │ │ ├── count_barcodes_mapped.py │ │ ├── count_barcodes_transcriptomic.py │ │ ├── create_config_file.py │ │ ├── generate_star_index.py │ │ ├── map_with_star.py │ │ ├── pipeline.py │ │ ├── process_reads.py │ │ └── quantify_gene_expression.py │ ├── config.py │ ├── expression.pyx │ ├── gcloud.py │ ├── mapping.py │ ├── pipeline.py │ ├── quantify_transcript_expression.py │ └── reads.pyx ├── qc │ ├── __init__.py │ ├── general.py │ └── saturation.py └── util.py └── tests ├── conftest.py └── indrop ├── conftest.py ├── test_barcodes.py ├── test_config.py ├── test_expression.py ├── test_mapping.py └── test_reads.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/singlecell/HEAD/.gitignore -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/singlecell/HEAD/AUTHORS -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/flo-compbio/singlecell/HEAD/LICENSE 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