.gitignore
CITATION.cff
LICENSE
MANIFEST.in
README.md
README.rst
__init__.py
pyproject.toml
setup.py
docs/Makefile
docs/make.bat
docs/source/conf.py
docs/source/index.rst
pycrispr/__init__.py
pycrispr.egg-info/PKG-INFO
pycrispr.egg-info/SOURCES.txt
pycrispr.egg-info/dependency_links.txt
pycrispr.egg-info/entry_points.txt
pycrispr.egg-info/requires.txt
pycrispr.egg-info/top_level.txt
pycrispr/scripts/__init__.py
pycrispr/scripts/pycrispr.py
pycrispr/scripts/src/count.yaml
pycrispr/scripts/src/flute.R
pycrispr/scripts/src/flute.yaml
pycrispr/scripts/src/join.yaml
pycrispr/scripts/src/snakefile
pycrispr/scripts/src/stats.yaml
pycrispr/scripts/src/trim.yaml
pycrispr/scripts/src/python/bagel2bf.py
pycrispr/scripts/src/python/bagel2fc.py
pycrispr/scripts/src/python/bagel2pr.py
pycrispr/scripts/src/python/convert_count_table.py
pycrispr/scripts/src/python/join.py
pycrispr/scripts/src/python/plot.py
pycrispr/scripts/src/python/plot_bf.py
pycrispr/scripts/src/python/plot_pr.py
pycrispr/scripts/src/report/alignment-rates.rst
pycrispr/scripts/src/report/bagel2.rst
pycrispr/scripts/src/report/bagel2_plots.rst
pycrispr/scripts/src/report/dot-plot_neg.rst
pycrispr/scripts/src/report/dot-plot_pos.rst
pycrispr/scripts/src/report/mageck.rst
pycrispr/scripts/src/report/multiqc.rst
pycrispr/scripts/src/report/plot-coverage.rst
pycrispr/scripts/src/report/report.rst
pycrispr/scripts/src/report/sgrank.rst
pycrispr/scripts/src/report/volcano.rst