.gitignore
LICENSE
MANIFEST.in
README.md
environment_bean.yml
pyproject.toml
requirements.txt
setup.py
.github/workflows/CI.yml
.github/workflows/documentation.yml
.github/workflows/pypi_release.yml
bean/__init__.py
bean/annotate/__init__.py
bean/annotate/_supporting_fn.py
bean/annotate/filter_alleles.py
bean/annotate/ldlr_exons.fa
bean/annotate/translate_allele.py
bean/annotate/utils.py
bean/cli/__init__.py
bean/cli/count.py
bean/cli/count_samples.py
bean/cli/create_screen.py
bean/cli/execute.py
bean/cli/filter.py
bean/cli/get_splice_sites.py
bean/cli/profile.py
bean/cli/qc.py
bean/cli/run.py
bean/framework/AminoAcidEdit.py
bean/framework/Edit.py
bean/framework/ReporterScreen.py
bean/framework/__init__.py
bean/framework/allele_counts.py
bean/framework/parser.py
bean/framework/read_from_csvs.py
bean/framework/__pycache__/ReporterScreen_.py
bean/mapping/CRISPResso2Align.c
bean/mapping/CRISPResso2Align.pyx
bean/mapping/GuideEditCounter.py
bean/mapping/__init__.py
bean/mapping/_supporting_fn.py
bean/mapping/utils.py
bean/model/__init__.py
bean/model/model.py
bean/model/parser.py
bean/model/readwrite.py
bean/model/run.py
bean/model/survival_model.py
bean/model/utils.py
bean/notebooks/profile_editing_preference.ipynb
bean/notebooks/sample_quality_report.ipynb
bean/plotting/__init__.py
bean/plotting/allele_stats.py
bean/plotting/editing_patterns.py
bean/plotting/parser.py
bean/plotting/utils.py
bean/preprocessing/__init__.py
bean/preprocessing/data_class.py
bean/preprocessing/get_alpha0.py
bean/preprocessing/get_pi_alpha0.py
bean/preprocessing/utils.py
bean/qc/__init__.py
bean/qc/guide_qc.py
bean/qc/parser.py
bean/qc/sample_qc.py
bean/qc/utils.py
bean/utils/__init__.py
bean/utils/arithmetric.py
bean/utils/plot.py
bin/bean
crispr_bean.egg-info/PKG-INFO
crispr_bean.egg-info/SOURCES.txt
crispr_bean.egg-info/dependency_links.txt
crispr_bean.egg-info/requires.txt
crispr_bean.egg-info/top_level.txt
docs/Makefile
docs/ReporterScreen_api.ipynb
docs/ReporterScreen_api.rst
docs/_count.md
docs/_create-screen.md
docs/_filter.md
docs/_get_splice_sites.md
docs/_input.md
docs/_profile.md
docs/_qc.md
docs/_reporterscreen.md
docs/_run.md
docs/_tutorial_cds.md
docs/_tutorial_gwas.md
docs/_tutorial_no_edit.md
docs/_tutorial_prolif_gwas.md
docs/conf.py
docs/count.rst
docs/count_samples.rst
docs/create_screen.rst
docs/editing_pattern_analysis.ipynb
docs/exon_fa_format.md
docs/filter.rst
docs/index.rst
docs/input.rst
docs/make.bat
docs/profile.rst
docs/qc.rst
docs/qc_report_LDLvar.html
docs/qc_report_LDLvar.ipynb
docs/reporterscreen.rst
docs/requirements.txt
docs/run.rst
docs/sample_quality_report.ipynb
docs/subcommands.rst
docs/tutorial_cds.rst
docs/tutorial_gwas.rst
docs/tutorial_no_edit.rst
docs/tutorial_prolif_gwas.rst
docs/tutorials.rst
docs/assets/bean.gif
docs/assets/bean_title2.svg
docs/assets/beans.svg
docs/assets/beans_32.ico
docs/assets/dag_bean_v2.svg
docs/assets/data_structure_v2.png
docs/assets/library_design.png
docs/assets/model_output.png
docs/assets/output_20_2.png
docs/assets/output_34_1.png
docs/assets/profile_output.png
docs/assets/proliferation.png
docs/assets/qc_output.png
docs/assets/screendata.svg
docs/assets/sequence_struct.png
docs/assets/sorting_bins@8x.png
docs/assets/summary.png
docs/assets/summary.svg
docs/assets/tiling.png
docs/assets/translation.png
docs/assets/variant.png
docs/example_filtering_output/my_sorting_screen_masked.filtered.filter_log.txt
docs/example_filtering_output/my_sorting_screen_masked.filtered.filtered_allele_stats.pdf
tests/test_Edit.py
tests/test_count.py
tests/test_create.py
tests/test_filter.py
tests/test_profile.py
tests/test_qc.py
tests/test_run.py
tests/CRISPRessoCount_on_test/CRISPRessoCount_RUNNING_LOG.txt
tests/data/accessibility_signal.bw
tests/data/accessibility_signal_chr6.bw
tests/data/bean_count_test_screen.h5ad
tests/data/gene_symbols.txt
tests/data/ldlr_exons.fa
tests/data/sample_list.csv
tests/data/sample_list_survival.csv
tests/data/sample_list_tiling.csv
tests/data/survival_var_mini_screen.h5ad
tests/data/test_R1.fastq
tests/data/test_R2.fastq
tests/data/test_guide_info.csv
tests/data/test_guide_info_tiling.csv
tests/data/test_guide_info_tiling_chrom.csv
tests/data/test_tiling_R1.fastq
tests/data/test_tiling_R2.fastq
tests/data/tiling_mini_screen.h5ad
tests/data/tiling_mini_screen_missing.h5ad
tests/data/var_mini_counts.csv
tests/data/var_mini_guides.csv
tests/data/var_mini_samples.csv
tests/data/var_mini_screen.h5ad
tests/data/var_mini_screen_annotated.translation_ref_mismatches.csv
tests/data/var_mini_screen_dual.h5ad
tests/data/var_mini_screen_missing.h5ad
tests/data/fastq/rep1_bot_R1.fastq
tests/data/fastq/rep1_bot_R2.fastq
tests/data/fastq/rep1_bulk_R1.fastq
tests/data/fastq/rep1_bulk_R2.fastq
tests/data/fastq/rep1_top_R1.fastq
tests/data/fastq/rep1_top_R2.fastq
tests/data/fastq/rep2_bot_R1.fastq
tests/data/fastq/rep2_bot_R2.fastq
tests/data/fastq/rep2_bulk_R1.fastq
tests/data/fastq/rep2_bulk_R2.fastq
tests/data/fastq/rep2_top_R1.fastq
tests/data/fastq/rep2_top_R2.fastq
tests/data/fastq/rep3_bot_R1.fastq
tests/data/fastq/rep3_bot_R2.fastq
tests/data/fastq/rep3_bulk_R1.fastq
tests/data/fastq/rep3_bulk_R2.fastq
tests/data/fastq/rep3_top_R1.fastq
tests/data/fastq/rep3_top_R2.fastq
tests/data/fastq/rep4_bot_R1.fastq
tests/data/fastq/rep4_bot_R2.fastq
tests/data/fastq/rep4_bulk_R1.fastq
tests/data/fastq/rep4_bulk_R2.fastq
tests/data/fastq/rep4_top_R1.fastq
tests/data/fastq/rep4_top_R2.fastq
tests/test_res/.gitkeep