python-scripts/knock-knock
site-packages/knock_knock-0.8.2.dist-info/INSTALLER
site-packages/knock_knock-0.8.2.dist-info/METADATA
site-packages/knock_knock-0.8.2.dist-info/RECORD
site-packages/knock_knock-0.8.2.dist-info/REQUESTED
site-packages/knock_knock-0.8.2.dist-info/WHEEL
site-packages/knock_knock-0.8.2.dist-info/direct_url.json
site-packages/knock_knock-0.8.2.dist-info/entry_points.txt
site-packages/knock_knock-0.8.2.dist-info/licenses/LICENSE
site-packages/knock_knock-0.8.2.dist-info/top_level.txt
site-packages/knock_knock/__init__.py
site-packages/knock_knock/architecture/ENDseq.py
site-packages/knock_knock/architecture/HDR.py
site-packages/knock_knock/architecture/__init__.py
site-packages/knock_knock/architecture/integrase.py
site-packages/knock_knock/architecture/prime_editing.py
site-packages/knock_knock/architecture/twin_prime.py
site-packages/knock_knock/architecture/uditas.py
site-packages/knock_knock/arrayed_experiment_group.py
site-packages/knock_knock/blast.py
site-packages/knock_knock/build_strategies.py
site-packages/knock_knock/cli.py
site-packages/knock_knock/demultiplex_by_genotype.py
site-packages/knock_knock/editing_strategy.py
site-packages/knock_knock/effector.py
site-packages/knock_knock/example_data/data/illumina/BCAP31_ultramer_R1.fastq.gz
site-packages/knock_knock/example_data/data/illumina/BCAP31_ultramer_R2.fastq.gz
site-packages/knock_knock/example_data/data/illumina/CLTA_PCR_R1.fastq.gz
site-packages/knock_knock/example_data/data/illumina/CLTA_PCR_R2.fastq.gz
site-packages/knock_knock/example_data/data/illumina/sample_sheet.csv
site-packages/knock_knock/example_data/data/pacbio/RAB11A_PCR.fastq.gz
site-packages/knock_knock/example_data/data/pacbio/RAB11A_plasmid.fastq.gz
site-packages/knock_knock/example_data/data/pacbio/sample_sheet.csv
site-packages/knock_knock/example_data/strategies/amplicon_primers.csv
site-packages/knock_knock/example_data/strategies/donors.csv
site-packages/knock_knock/example_data/strategies/sgRNAs.csv
site-packages/knock_knock/example_data/strategies/targets.csv
site-packages/knock_knock/experiment.py
site-packages/knock_knock/experiment_group.py
site-packages/knock_knock/explore.py
site-packages/knock_knock/illumina_experiment.py
site-packages/knock_knock/integrases.py
site-packages/knock_knock/lengths.py
site-packages/knock_knock/logo_v2.png
site-packages/knock_knock/nanopore_experiment.py
site-packages/knock_knock/outcome.py
site-packages/knock_knock/pacbio_experiment.py
site-packages/knock_knock/parallel.py
site-packages/knock_knock/pegRNAs.py
site-packages/knock_knock/ranges.py
site-packages/knock_knock/recombination.py
site-packages/knock_knock/svg.py
site-packages/knock_knock/table.py
site-packages/knock_knock/table_template/conf.json
site-packages/knock_knock/table_template/table.html.j2
site-packages/knock_knock/test/.gitignore
site-packages/knock_knock/test/HDR/strategies/HDR_pacbio_R_PCR/RAB11A-150HA_PCR_donor.gb
site-packages/knock_knock/test/HDR/strategies/HDR_pacbio_R_PCR/RAB11A_PAC.gb
site-packages/knock_knock/test/HDR/strategies/HDR_pacbio_R_PCR/parameters.yaml
site-packages/knock_knock/test/HDR/strategies/HDR_pacbio_R_PCR/sgRNAs.csv
site-packages/knock_knock/test/HDR/test_homology_arm_inference.py
site-packages/knock_knock/test/__init__.py
site-packages/knock_knock/test/categorization/__init__.py
site-packages/knock_knock/test/categorization/data/HDR_WGS_EEA1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/HDR_WGS_EEA1/extracted_CCS.fastq
site-packages/knock_knock/test/categorization/data/HDR_WGS_EEA1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/HDR_WGS_VPS35/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/HDR_WGS_VPS35/extracted_CCS.fastq
site-packages/knock_knock/test/categorization/data/HDR_WGS_VPS35/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/HDR_illumina_B_ULT/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/HDR_illumina_B_ULT/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/HDR_illumina_B_ULT/extracted_R2.fastq
site-packages/knock_knock/test/categorization/data/HDR_illumina_B_ULT/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_PCR/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_PCR/extracted_CCS.fastq
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_PCR/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_plasmid/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_plasmid/extracted_CCS.fastq
site-packages/knock_knock/test/categorization/data/HDR_pacbio_R_plasmid/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_EMX1_+014_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_EMX1_+014_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_EMX1_+014_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_HEK3_+026_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_HEK3_+026_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig3B_HEK3_+026_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-5_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-5_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-5_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-80_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-80_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4G_HEK3_del1-80_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1AC_6GT_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1AC_6GT_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1AC_6GT_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1Tins_6GA_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1Tins_6GA_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_FANCF_1Tins_6GA_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_HEK3_1CTTins_5Gdel_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_HEK3_1CTTins_5Gdel_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_HEK3_1CTTins_5Gdel_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_RNF2_1CA_5GT_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_RNF2_1CA_5GT_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID31634902_Fig4H_RNF2_1CA_5GT_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig1C_HEK3_attB_A30_B30_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig1C_HEK3_attB_A30_B30_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig1C_HEK3_attB_A30_B30_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-1696+1697_46_22_epegRNA_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-1696+1697_46_22_epegRNA_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-1696+1697_46_22_epegRNA_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-E4fe+1687_64_24_epegRNA_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-E4fe+1687_64_24_epegRNA_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2C_PAH-E4fe+1687_64_24_epegRNA_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_HA_64_EvoPreQ1_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_HA_64_EvoPreQ1_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_HA_64_EvoPreQ1_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_PD_90_standard_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_PD_90_standard_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig2E_HEK3_PD_90_standard_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1651+1652_A1246c_B1376a_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1651+1652_A1246c_B1376a_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1651+1652_A1246c_B1376a_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1653+1715_A1615a_B1676a_1/expected_categorizations.yaml
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1653+1715_A1615a_B1676a_1/extracted_R1.fastq
site-packages/knock_knock/test/categorization/data/PMID34887556_Fig3C_AAVS1-1653+1715_A1615a_B1676a_1/sample_sheet.csv
site-packages/knock_knock/test/categorization/results/.gitignore
site-packages/knock_knock/test/categorization/results/HDR_WGS_EEA1/alignment_extracted/CCS_by_name.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_WGS_EEA1/alignment_extracted/CCS_by_name_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/HDR_WGS_VPS35/alignment_extracted/CCS_by_name.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_WGS_VPS35/alignment_extracted/CCS_by_name_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/R1_no_overlap.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/R2_no_overlap.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/lengths.hdf5
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/outcome_counts.csv
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/outcome_list.txt
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/outcomes/sanitized_category_names.txt
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/trimmed.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/common_sequences/trimmed_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/stitched.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/stitched_lengths.csv
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/stitched_uncommon.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/stitched_uncommon_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/HDR_illumina_B_ULT/alignment_extracted/too_short_outcome_list.txt
site-packages/knock_knock/test/categorization/results/HDR_pacbio_R_PCR/alignment_extracted/CCS_by_name.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_pacbio_R_PCR/alignment_extracted/CCS_by_name_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/HDR_pacbio_R_plasmid/alignment_extracted/CCS_by_name.fastq.gz
site-packages/knock_knock/test/categorization/results/HDR_pacbio_R_plasmid/alignment_extracted/CCS_by_name_combined_alignments.by_name.bam
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/lengths.hdf5
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/outcome_counts.csv
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/outcome_list.txt
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/outcomes/sanitized_category_names.txt
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/trimmed.fastq.gz
site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_EMX1_+014_1/alignment_extracted/common_sequences/trimmed_combined_alignments.by_name.bam
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site-packages/knock_knock/test/categorization/results/PMID31634902_Fig3B_HEK3_+026_1/alignment_extracted/common_sequences/lengths.hdf5
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