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.gitignore
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.gitignore
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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Package setup
*.egg-info
/build
/dist
# Sphinx documentation
docs/build/*
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# IPython
profile_default/
ipython_config.py
# Environments
.env
.venv
.python-version
env/
venv/
ENV/
# mypy
.mypy_cache/
.dmypy.json
dmypy.json
# Ruff
.ruff_cache/
# Pyre type checker
.pyre/
# Ignore TODO list
TODO.md
CHANGELOG.md
/.trash
# Ignore testing cache
.pytest_cache
# coverage files
coverage.xml
.coverage
docs/coverage_report/*
# Keep folders indicated by .gitkeep
!/**/.gitkeep
!/**/.gitignore
requirements.dev.txt
manuscript.pdf
/data/rpgn_example/
/rpgn/
/benchmark/
# All .DS_Store files
**/.DS_Store
docs/source/.pybiomart.sqlite
test/data/fabry_disease/counts_pytximport_lengthScaledTPM.csv
test/data/fabry_disease/counts_pytximport_no.csv
test/data/fabry_disease/counts_pytximport_scaledTPM.csv
test/data/fabry_disease/counts_pytximport.csv
test/data/salmon/quant.h5ad
.pybiomart.sqlite
test/data/salmon/counts_pytximport_dtuScaledTPM.csv
docs/source/transcript_gene_map.tsv