LICENSE
README.md
pyproject.toml
src/MitoRiboPy.egg-info/PKG-INFO
src/MitoRiboPy.egg-info/SOURCES.txt
src/MitoRiboPy.egg-info/dependency_links.txt
src/MitoRiboPy.egg-info/entry_points.txt
src/MitoRiboPy.egg-info/requires.txt
src/MitoRiboPy.egg-info/top_level.txt
src/mitoribopy/__init__.py
src/mitoribopy/__main__.py
src/mitoribopy/console.py
src/mitoribopy/progress.py
src/mitoribopy/align/__init__.py
src/mitoribopy/align/_types.py
src/mitoribopy/align/adapter_detect.py
src/mitoribopy/align/align.py
src/mitoribopy/align/bam_utils.py
src/mitoribopy/align/contam.py
src/mitoribopy/align/dedup.py
src/mitoribopy/align/read_counts.py
src/mitoribopy/align/sample_resolve.py
src/mitoribopy/align/tool_check.py
src/mitoribopy/align/trim.py
src/mitoribopy/analysis/__init__.py
src/mitoribopy/analysis/codon_correlation.py
src/mitoribopy/analysis/offset_enrichment.py
src/mitoribopy/analysis/offset_selection.py
src/mitoribopy/analysis/rna_seq.py
src/mitoribopy/analysis/translation_profile_analysis.py
src/mitoribopy/cli/__init__.py
src/mitoribopy/cli/align.py
src/mitoribopy/cli/all_.py
src/mitoribopy/cli/common.py
src/mitoribopy/cli/rnaseq.py
src/mitoribopy/cli/rpf.py
src/mitoribopy/config/__init__.py
src/mitoribopy/config/runtime.py
src/mitoribopy/data/__init__.py
src/mitoribopy/data/codon_tables.json
src/mitoribopy/data/codon_tables.py
src/mitoribopy/data/human_annotation.csv
src/mitoribopy/data/reference_data.py
src/mitoribopy/data/transcript_annotations.py
src/mitoribopy/data/yeast_annotation.csv
src/mitoribopy/io/__init__.py
src/mitoribopy/io/bam_reader.py
src/mitoribopy/io/bed_reader.py
src/mitoribopy/io/read_counts.py
src/mitoribopy/pipeline/__init__.py
src/mitoribopy/pipeline/context.py
src/mitoribopy/pipeline/runner.py
src/mitoribopy/pipeline/steps.py
src/mitoribopy/plotting/__init__.py
src/mitoribopy/plotting/coverage_profile_plots.py
src/mitoribopy/plotting/igv_export.py
src/mitoribopy/plotting/structure_density_export.py
src/mitoribopy/plotting/style.py
src/mitoribopy/plotting/translation_profile_plots.py
src/mitoribopy/plotting/visualization.py
src/mitoribopy/rnaseq/__init__.py
src/mitoribopy/rnaseq/_types.py
src/mitoribopy/rnaseq/alignment.py
src/mitoribopy/rnaseq/counts.py
src/mitoribopy/rnaseq/de_analysis.py
src/mitoribopy/rnaseq/de_loader.py
src/mitoribopy/rnaseq/fastq_pairing.py
src/mitoribopy/rnaseq/gene_ids.py
src/mitoribopy/rnaseq/plots.py
src/mitoribopy/rnaseq/reference_gate.py
src/mitoribopy/rnaseq/split_replicates.py
src/mitoribopy/rnaseq/te.py
src/mitoribopy/rnaseq/umi_detect.py
src/mitoribopy/tools/__init__.py
src/mitoribopy/tools/read_composition.py
src/mitoribopy/tools/subsample.py
src/mitoribopy/tools/subsample_fastq.py
tests/test_align_adapter_detect.py
tests/test_align_align.py
tests/test_align_bam_utils.py
tests/test_align_cli.py
tests/test_align_contam.py
tests/test_align_dedup.py
tests/test_align_integration.py
tests/test_align_read_counts.py
tests/test_align_resume.py
tests/test_align_sample_overrides.py
tests/test_align_sample_resolve.py
tests/test_align_tool_check.py
tests/test_align_trim.py
tests/test_all_cli.py
tests/test_analysis_sites.py
tests/test_bam_reader.py
tests/test_cli.py
tests/test_cli_subcommands.py
tests/test_codon_tables.py
tests/test_config_runtime.py
tests/test_defensive_guards.py
tests/test_integration_pipeline.py
tests/test_offset_per_sample.py
tests/test_pipeline_arg_aliases.py
tests/test_progress.py
tests/test_read_counts.py
tests/test_read_length_consistency.py
tests/test_reference_data.py
tests/test_rnaseq.py
tests/test_rnaseq_alignment_helpers.py
tests/test_rnaseq_cli.py
tests/test_rnaseq_cli_from_fastq.py
tests/test_rnaseq_de_analysis.py
tests/test_rnaseq_extra_plots.py
tests/test_rnaseq_fastq_pairing.py
tests/test_rnaseq_split_replicates.py
tests/test_rnaseq_umi_detect.py
tests/test_rpf_count_filter.py
tests/test_subsample.py
tests/test_visualization.py