.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/config.py
spacemake/errors.py
spacemake/parallel.py
spacemake/project_df.py
spacemake/reporting.py
spacemake/smk.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/data/visium_barcode_positions.csv
spacemake/data/config/config.yaml
spacemake/data/config/longread.yaml
spacemake/data/config/species_data_url.yaml
spacemake/longread/__main__.py
spacemake/longread/align.py
spacemake/longread/annotation.py
spacemake/longread/cache.py
spacemake/longread/cmdline.py
spacemake/longread/overview.py
spacemake/longread/report.py
spacemake/longread/util.py
spacemake/preprocess/__init__.py
spacemake/preprocess/cmdline.py
spacemake/preprocess/dge.py
spacemake/preprocess/fastq.py
spacemake/snakemake/downsample.smk
spacemake/snakemake/dropseq.smk
spacemake/snakemake/main.smk
spacemake/snakemake/merge_samples.smk
spacemake/snakemake/pacbio.smk
spacemake/snakemake/species_init.smk
spacemake/snakemake/visium.smk
spacemake/snakemake/scripts/automated_analysis.py
spacemake/snakemake/scripts/automated_analysis_create_processed_data_files.py
spacemake/snakemake/scripts/automated_analysis_create_report.Rmd
spacemake/snakemake/scripts/clean_top_barcodes.py
spacemake/snakemake/scripts/create_sample_db.R
spacemake/snakemake/scripts/create_sample_overview.Rmd
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/parse_ribo_log.py
spacemake/snakemake/scripts/qc_sequencing_create_sheet.Rmd
spacemake/snakemake/scripts/saturation_analysis.Rmd
spacemake/snakemake/scripts/shared_functions.R
spacemake/snakemake/scripts/snakemake_helper_functions.py
spacemake/snakemake/scripts/split_reads_by_strand_info.py
spacemake/spatial/__init__.py
spacemake/spatial/novosparc_reconstruction.py
spacemake/spatial/util.py