.readthedocs.yaml
COPYING
LICENSE
MANIFEST.in
README.md
environment.yaml
pyproject.toml
setup.cfg
setup.py
docs/conf.py
spacemake/__init__.py
spacemake/alnstats.py
spacemake/annotator.py
spacemake/cmdline.py
spacemake/config.py
spacemake/contrib.py
spacemake/errors.py
spacemake/map_strategy.py
spacemake/migrate.py
spacemake/parallel.py
spacemake/plotting.py
spacemake/project_df.py
spacemake/quant.py
spacemake/reporting.py
spacemake/smk.py
spacemake/tag_alignments.py
spacemake/unittests.py
spacemake/util.py
spacemake.egg-info/PKG-INFO
spacemake.egg-info/SOURCES.txt
spacemake.egg-info/dependency_links.txt
spacemake.egg-info/entry_points.txt
spacemake.egg-info/not-zip-safe
spacemake.egg-info/top_level.txt
spacemake/bin/BamTagHistogram.py
spacemake/bin/fastq_to_uBAM.py
spacemake/data/visium_barcode_positions.csv
spacemake/data/config/config.yaml
spacemake/data/config/longread.yaml
spacemake/data/config/species_data_url.yaml
spacemake/data/puck_collection/create_novaseq_S4_coordinate_system.py
spacemake/data/puck_collection/openst_coordinate_system.csv
spacemake/data/test/test_bc1.csv
spacemake/data/test/test_bc2.csv
spacemake/longread/__main__.py
spacemake/longread/annotation.py
spacemake/longread/cache.py
spacemake/longread/cmdline.py
spacemake/longread/overview.py
spacemake/longread/report.py
spacemake/longread/signature.py
spacemake/preprocess/__init__.py
spacemake/preprocess/cmdline.py
spacemake/preprocess/dge.py
spacemake/report/__init__.py
spacemake/report/saturation_analysis.py
spacemake/report/utils.py
spacemake/report/notebooks/automated_analysis.ipynb
spacemake/report/notebooks/qc_sheet.ipynb
spacemake/report/notebooks/saturation_analysis.ipynb
spacemake/report/scripts/inject_navigation.sh
spacemake/report/static/navigation.css
spacemake/report/static/navigation.js
spacemake/report/templates/automated_analysis_nbtemplate.html.j2
spacemake/snakemake/__init__.py
spacemake/snakemake/downsample.smk
spacemake/snakemake/dropseq.smk
spacemake/snakemake/longread.smk
spacemake/snakemake/main.smk
spacemake/snakemake/mapping.smk
spacemake/snakemake/merge_samples.smk
spacemake/snakemake/migrate.smk
spacemake/snakemake/species_init.smk
spacemake/snakemake/variables.py
spacemake/snakemake/visium.smk
spacemake/snakemake/scripts/clean_top_barcodes.py
spacemake/snakemake/scripts/create_spatial_barcode_file.py
spacemake/snakemake/scripts/create_spatial_dge.py
spacemake/snakemake/scripts/filter_mm_reads.py
spacemake/snakemake/scripts/fix_bam_header.py
spacemake/snakemake/scripts/kmer_stats_from_fastq.py
spacemake/snakemake/scripts/n_intersect_sequences.py
spacemake/snakemake/scripts/parse_ribo_log.py
spacemake/snakemake/scripts/snakemake_helper_functions.py
spacemake/snakemake/scripts/splice_bam_header.py
spacemake/snakemake/scripts/split_reads_by_strand_info.py
spacemake/spatial/__init__.py
spacemake/spatial/cmdline.py
spacemake/spatial/he_integration.py
spacemake/spatial/novosparc_integration.py
spacemake/spatial/puck_collection.py
spacemake/spatial/util.py
test_data/make_chr22_test_data.py
test_data/test_config.yaml
test_data/test_coordinate_system.csv
test_data/test_project_df.csv
tests/fixtures.py
tests/test_cmdline.py
tests/test_fastq_to_ubam.py
tests/test_map_strategy.py