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CITATION.cff
CODE_OF_CONDUCT.md
LICENSE
README.md
TODO.md
mkdocs.yml
pyproject.toml
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.github/ISSUE_TEMPLATE/feature_request.yaml
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docs/extending.md
docs/index.md
docs/installation.md
docs/introduction.md
docs/links.md
docs/usage.md
docs/workflow.md
docs/api/index.md
docs/api/io.md
docs/api/isoslam.md
docs/api/logging.md
docs/api/plotting.md
docs/api/processing.md
docs/api/summary.md
docs/api/utils.md
docs/contributing/adding_modules.md
docs/contributing/index.md
docs/contributing/profiling.md
isoslam/__init__.py
isoslam/_version.py
isoslam/all_introns_counts_and_info.py
isoslam/default_config.yaml
isoslam/io.py
isoslam/isoslam.py
isoslam/logging.py
isoslam/pipeline_slam_3UIs.py
isoslam/plotting.py
isoslam/processing.py
isoslam/summary.py
isoslam/utils.py
isoslam/validation.py
isoslam.egg-info/PKG-INFO
isoslam.egg-info/SOURCES.txt
isoslam.egg-info/dependency_links.txt
isoslam.egg-info/entry_points.txt
isoslam.egg-info/requires.txt
isoslam.egg-info/top_level.txt
isoslam/pipeline_slam_3UIs/all_introns_counts_and_info.py
isoslam/pipeline_slam_3UIs/pipeline.yml
isoslam/pipeline_slam_3UIs/summarize_counts.R
tests/__init__.py
tests/conftest.py
tests/test_all_introns_counts_and_info.py
tests/test_io.py
tests/test_isoslam.py
tests/test_processing.py
tests/test_summary.py
tests/test_utils.py
tests/test_validation.py
tests/_regtest_outputs/test_all_introns_counts_and_info.test_main[file_0hr1].out
tests/_regtest_outputs/test_all_introns_counts_and_info.test_main[file_no4sU].out
tests/_regtest_outputs/test_processing.test_process[0hr1].out
tests/_regtest_outputs/test_processing.test_process[no4sU].out
tests/_regtest_outputs/test_summary.test_aggregate_conversions[missing_conversion_True_for_transcript_id_on_chr_3].out
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tests/_regtest_outputs/test_summary.test_derive_weight_within_isoform[simple].out
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tests/_regtest_outputs/test_summary.test_extract_hour_and_replicate[simple].out
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tests/_regtest_outputs/test_summary.test_normalise[simple].out
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tests/_regtest_outputs/test_summary.test_remove_zero_baseline[real_(conversion_percent)].out
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tests/resources/test.yaml
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tests/resources/bam/d0_no4sU_filtered_remapped_sorted.bam
tests/resources/bam/d0_no4sU_filtered_remapped_sorted.bam.bai
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tests/resources/bam/sorted_assigned/d0_no4sU_filtered_remapped_sorted.sorted.assigned.bam
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tests/resources/bed6/test_coding_introns.bed
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