├── .gitignore ├── .pre-commit-config.yaml ├── MANIFEST.in ├── README.md ├── environment.yaml ├── pyproject.toml ├── setup.cfg └── src └── slideseq ├── __init__.py ├── alignment_quality.py ├── bead_matching.py ├── config.py ├── config.yaml ├── library.py ├── metadata.py ├── pipeline ├── __init__.py ├── alignment.py ├── downsampling.py ├── preparation.py ├── processing.py ├── reference.py ├── submit_slideseq.py └── write_matrix.py ├── plot ├── __init__.py ├── plot_downsampling.py └── plot_library_metrics.py ├── retag_bam.py ├── scripts ├── __init__.py ├── alignment.sh ├── barcode_matrix.py ├── build_reference.sh ├── check_barcodes.py ├── demultiplex.sh ├── downsampling.sh ├── plot_barcodes.py └── processing.sh └── util ├── __init__.py ├── constants.py ├── gutil.py ├── logger.py └── run_info.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/README.md -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/environment.yaml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/setup.cfg -------------------------------------------------------------------------------- /src/slideseq/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.3" 2 | -------------------------------------------------------------------------------- /src/slideseq/alignment_quality.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/alignment_quality.py -------------------------------------------------------------------------------- /src/slideseq/bead_matching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/bead_matching.py -------------------------------------------------------------------------------- /src/slideseq/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/config.py -------------------------------------------------------------------------------- /src/slideseq/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/config.yaml -------------------------------------------------------------------------------- /src/slideseq/library.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/library.py -------------------------------------------------------------------------------- /src/slideseq/metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/metadata.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/slideseq/pipeline/alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/alignment.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/downsampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/downsampling.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/preparation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/preparation.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/processing.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/reference.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/submit_slideseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/submit_slideseq.py -------------------------------------------------------------------------------- /src/slideseq/pipeline/write_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/pipeline/write_matrix.py -------------------------------------------------------------------------------- /src/slideseq/plot/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/plot/__init__.py -------------------------------------------------------------------------------- /src/slideseq/plot/plot_downsampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/plot/plot_downsampling.py -------------------------------------------------------------------------------- /src/slideseq/plot/plot_library_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/plot/plot_library_metrics.py -------------------------------------------------------------------------------- /src/slideseq/retag_bam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/retag_bam.py -------------------------------------------------------------------------------- /src/slideseq/scripts/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/__init__.py -------------------------------------------------------------------------------- /src/slideseq/scripts/alignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/alignment.sh -------------------------------------------------------------------------------- /src/slideseq/scripts/barcode_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/barcode_matrix.py -------------------------------------------------------------------------------- /src/slideseq/scripts/build_reference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/build_reference.sh -------------------------------------------------------------------------------- /src/slideseq/scripts/check_barcodes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/check_barcodes.py -------------------------------------------------------------------------------- /src/slideseq/scripts/demultiplex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/demultiplex.sh -------------------------------------------------------------------------------- /src/slideseq/scripts/downsampling.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/downsampling.sh -------------------------------------------------------------------------------- /src/slideseq/scripts/plot_barcodes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/plot_barcodes.py -------------------------------------------------------------------------------- /src/slideseq/scripts/processing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/scripts/processing.sh -------------------------------------------------------------------------------- /src/slideseq/util/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/util/__init__.py -------------------------------------------------------------------------------- /src/slideseq/util/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/util/constants.py -------------------------------------------------------------------------------- /src/slideseq/util/gutil.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/util/gutil.py -------------------------------------------------------------------------------- /src/slideseq/util/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/util/logger.py -------------------------------------------------------------------------------- /src/slideseq/util/run_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MacoskoLab/slideseq-tools/HEAD/src/slideseq/util/run_info.py --------------------------------------------------------------------------------