├── .circleci └── config.yml ├── .dockerignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── envs │ └── test_env.yml └── workflows │ ├── .pylintrc │ ├── aws_ecr.yml │ ├── integration_tests.yml │ ├── pylint.yml │ └── pytest.yml ├── .gitignore ├── CRISPResso2 ├── BLOSUM62 ├── CRISPResso2Align.c ├── CRISPResso2Align.pyx ├── CRISPRessoAggregateCORE.py ├── CRISPRessoBatchCORE.py ├── CRISPRessoCORE.py ├── CRISPRessoCOREResources.c ├── CRISPRessoCOREResources.pyx ├── CRISPRessoCompareCORE.py ├── CRISPRessoMetaCORE.py ├── CRISPRessoMultiProcessing.py ├── CRISPRessoPlot.py ├── CRISPRessoPooledCORE.py ├── CRISPRessoPooledWGSCompareCORE.py ├── CRISPRessoReports │ ├── .gitattributes │ ├── .github │ │ └── workflows │ │ │ ├── .pylintrc │ │ │ └── pylint.yml │ ├── CRISPRessoReport.py │ ├── README.md │ ├── __init__.py │ ├── jinja_partials.py │ └── templates │ │ ├── CRISPResso_justcup.png │ │ ├── batchReport.html │ │ ├── favicon.ico │ │ ├── layout.html │ │ ├── multiReport.html │ │ ├── pooledReport.html │ │ ├── report.html │ │ ├── shared │ │ └── partials │ │ │ ├── failed_runs.html │ │ │ ├── fig_reports.html │ │ │ ├── fig_summaries.html │ │ │ ├── guardrail_warnings.html │ │ │ ├── log_params.html │ │ │ └── report_footer_buttons.html │ │ └── wgsReport.html ├── CRISPRessoShared.py ├── CRISPRessoWGSCORE.py ├── EDNAFULL ├── README ├── __init__.py ├── args.json ├── default_style.json ├── filterFastqs.py ├── setupLocal.py └── setupLocal.sh ├── CRISPResso2_router.py ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── crispresso_schematic.png ├── pyproject.toml ├── scripts ├── Load Plots.ipynb ├── countHighQualityBases.py ├── count_sgRNA_specific_edits.py ├── filterReadsOnSequencePresence.py ├── plotAmbiguous.py ├── plotCustomAllelePlot.py └── reconstituteReads.py ├── setup.cfg ├── setup.py └── tests ├── Both.Cas9.fastq ├── Both.Cas9.fastq.hg38.bam ├── Both.Cas9.fastq.hg38.bam.bai ├── Both.Cas9.fastq.smallGenome.bam ├── Both.Cas9.fastq.smallGenome.bam.bai ├── Cas9.amplicons.txt ├── Cas9.regions.txt ├── FANC.Cas9.fastq ├── FANC.Untreated.fastq ├── FANC.batch ├── FANC.local.batch ├── HEK3.Cas9.fastq ├── Makefile ├── expectedResults ├── CRISPRessoBatch_on_FANC │ └── MODIFICATION_FREQUENCY_SUMMARY.txt ├── CRISPRessoCompare_on_Cas9_VS_Untreated │ └── Alleles_frequency_table_around_sgRNA_GGAATCCCTTCTGCAGCACC.txt ├── CRISPRessoPooled_on_Both.Cas9 │ └── SAMPLES_QUANTIFICATION_SUMMARY.txt ├── CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome │ └── SAMPLES_QUANTIFICATION_SUMMARY.txt ├── CRISPResso_on_FANC.Cas9 │ ├── CRISPResso_quantification_of_editing_frequency.txt │ └── Nucleotide_frequency_table.txt └── CRISPResso_on_params │ ├── CRISPResso_quantification_of_editing_frequency.txt │ └── FANC.Nucleotide_frequency_table.txt ├── smallGenome ├── smallGenome.1.bt2 ├── smallGenome.2.bt2 ├── smallGenome.3.bt2 ├── smallGenome.4.bt2 ├── smallGenome.fa ├── smallGenome.fa.fai ├── smallGenome.rev.1.bt2 └── smallGenome.rev.2.bt2 ├── testRelease.sh ├── test_be_df.txt └── unit_tests ├── README.md ├── test_CRISPResso2Align.py ├── test_CRISPRessoBatchCORE.py ├── test_CRISPRessoCORE.py ├── test_CRISPRessoCOREResources.py ├── test_CRISPRessoCompareCORE.py ├── test_CRISPRessoPooledCORE.py └── test_CRISPRessoShared.py /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.circleci/config.yml -------------------------------------------------------------------------------- /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/envs/test_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/envs/test_env.yml -------------------------------------------------------------------------------- /.github/workflows/.pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/workflows/.pylintrc -------------------------------------------------------------------------------- /.github/workflows/aws_ecr.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/workflows/aws_ecr.yml -------------------------------------------------------------------------------- /.github/workflows/integration_tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/workflows/integration_tests.yml -------------------------------------------------------------------------------- /.github/workflows/pylint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/workflows/pylint.yml -------------------------------------------------------------------------------- /.github/workflows/pytest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.github/workflows/pytest.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/.gitignore -------------------------------------------------------------------------------- /CRISPResso2/BLOSUM62: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/BLOSUM62 -------------------------------------------------------------------------------- /CRISPResso2/CRISPResso2Align.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPResso2Align.c -------------------------------------------------------------------------------- /CRISPResso2/CRISPResso2Align.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPResso2Align.pyx -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoAggregateCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoAggregateCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoBatchCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoBatchCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoCOREResources.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoCOREResources.c -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoCOREResources.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoCOREResources.pyx -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoCompareCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoCompareCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoMetaCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoMetaCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoMultiProcessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoMultiProcessing.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoPlot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoPlot.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoPooledCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoPooledCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoPooledWGSCompareCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/.gitattributes -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/.github/workflows/.pylintrc -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/.github/workflows/pylint.yml -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/CRISPRessoReport.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/README.md -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/jinja_partials.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/jinja_partials.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/CRISPResso_justcup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/CRISPResso_justcup.png -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/batchReport.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/batchReport.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/favicon.ico -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/layout.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/multiReport.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/multiReport.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/pooledReport.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/pooledReport.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/report.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/report.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/failed_runs.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_reports.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/fig_summaries.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/guardrail_warnings.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/guardrail_warnings.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/log_params.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/shared/partials/report_footer_buttons.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/shared/partials/report_footer_buttons.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoReports/templates/wgsReport.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoReports/templates/wgsReport.html -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoShared.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoShared.py -------------------------------------------------------------------------------- /CRISPResso2/CRISPRessoWGSCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/CRISPRessoWGSCORE.py -------------------------------------------------------------------------------- /CRISPResso2/EDNAFULL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/EDNAFULL -------------------------------------------------------------------------------- /CRISPResso2/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/README -------------------------------------------------------------------------------- /CRISPResso2/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /CRISPResso2/args.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/args.json -------------------------------------------------------------------------------- /CRISPResso2/default_style.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/default_style.json -------------------------------------------------------------------------------- /CRISPResso2/filterFastqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/filterFastqs.py -------------------------------------------------------------------------------- /CRISPResso2/setupLocal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/setupLocal.py -------------------------------------------------------------------------------- /CRISPResso2/setupLocal.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2/setupLocal.sh -------------------------------------------------------------------------------- /CRISPResso2_router.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/CRISPResso2_router.py -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/README.md -------------------------------------------------------------------------------- /crispresso_schematic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/crispresso_schematic.png -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/pyproject.toml -------------------------------------------------------------------------------- /scripts/Load Plots.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/Load Plots.ipynb -------------------------------------------------------------------------------- /scripts/countHighQualityBases.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/countHighQualityBases.py -------------------------------------------------------------------------------- /scripts/count_sgRNA_specific_edits.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/count_sgRNA_specific_edits.py -------------------------------------------------------------------------------- /scripts/filterReadsOnSequencePresence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/filterReadsOnSequencePresence.py -------------------------------------------------------------------------------- /scripts/plotAmbiguous.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/plotAmbiguous.py -------------------------------------------------------------------------------- /scripts/plotCustomAllelePlot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/plotCustomAllelePlot.py -------------------------------------------------------------------------------- /scripts/reconstituteReads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/scripts/reconstituteReads.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [global] 2 | zip_ok = False 3 | no-use-wheel = true 4 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/setup.py -------------------------------------------------------------------------------- /tests/Both.Cas9.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Both.Cas9.fastq -------------------------------------------------------------------------------- /tests/Both.Cas9.fastq.hg38.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Both.Cas9.fastq.hg38.bam -------------------------------------------------------------------------------- /tests/Both.Cas9.fastq.hg38.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Both.Cas9.fastq.hg38.bam.bai -------------------------------------------------------------------------------- /tests/Both.Cas9.fastq.smallGenome.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Both.Cas9.fastq.smallGenome.bam -------------------------------------------------------------------------------- /tests/Both.Cas9.fastq.smallGenome.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Both.Cas9.fastq.smallGenome.bam.bai -------------------------------------------------------------------------------- /tests/Cas9.amplicons.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Cas9.amplicons.txt -------------------------------------------------------------------------------- /tests/Cas9.regions.txt: -------------------------------------------------------------------------------- 1 | chr9 962 1198 HEK3 2 | chr11 1024 1274 FANCF 3 | -------------------------------------------------------------------------------- /tests/FANC.Cas9.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/FANC.Cas9.fastq -------------------------------------------------------------------------------- /tests/FANC.Untreated.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/FANC.Untreated.fastq -------------------------------------------------------------------------------- /tests/FANC.batch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/FANC.batch -------------------------------------------------------------------------------- /tests/FANC.local.batch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/FANC.local.batch -------------------------------------------------------------------------------- /tests/HEK3.Cas9.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/HEK3.Cas9.fastq -------------------------------------------------------------------------------- /tests/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/Makefile -------------------------------------------------------------------------------- /tests/expectedResults/CRISPRessoBatch_on_FANC/MODIFICATION_FREQUENCY_SUMMARY.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPRessoBatch_on_FANC/MODIFICATION_FREQUENCY_SUMMARY.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPRessoCompare_on_Cas9_VS_Untreated/Alleles_frequency_table_around_sgRNA_GGAATCCCTTCTGCAGCACC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPRessoCompare_on_Cas9_VS_Untreated/Alleles_frequency_table_around_sgRNA_GGAATCCCTTCTGCAGCACC.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPRessoPooled_on_Both.Cas9/SAMPLES_QUANTIFICATION_SUMMARY.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPRessoPooled_on_Both.Cas9/SAMPLES_QUANTIFICATION_SUMMARY.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/SAMPLES_QUANTIFICATION_SUMMARY.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/SAMPLES_QUANTIFICATION_SUMMARY.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPResso_on_FANC.Cas9/CRISPResso_quantification_of_editing_frequency.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPResso_on_FANC.Cas9/CRISPResso_quantification_of_editing_frequency.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPResso_on_FANC.Cas9/Nucleotide_frequency_table.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPResso_on_FANC.Cas9/Nucleotide_frequency_table.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPResso_on_params/CRISPResso_quantification_of_editing_frequency.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPResso_on_params/CRISPResso_quantification_of_editing_frequency.txt -------------------------------------------------------------------------------- /tests/expectedResults/CRISPResso_on_params/FANC.Nucleotide_frequency_table.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/expectedResults/CRISPResso_on_params/FANC.Nucleotide_frequency_table.txt -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.1.bt2 -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.2.bt2 -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.3.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.3.bt2 -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.4.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.4.bt2 -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.fa -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.fa.fai -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.rev.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.rev.1.bt2 -------------------------------------------------------------------------------- /tests/smallGenome/smallGenome.rev.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/smallGenome/smallGenome.rev.2.bt2 -------------------------------------------------------------------------------- /tests/testRelease.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/testRelease.sh -------------------------------------------------------------------------------- /tests/test_be_df.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/test_be_df.txt -------------------------------------------------------------------------------- /tests/unit_tests/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/README.md -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPResso2Align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPResso2Align.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoBatchCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoBatchCORE.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoCORE.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoCOREResources.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoCOREResources.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoCompareCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoCompareCORE.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoPooledCORE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoPooledCORE.py -------------------------------------------------------------------------------- /tests/unit_tests/test_CRISPRessoShared.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pinellolab/CRISPResso2/HEAD/tests/unit_tests/test_CRISPRessoShared.py --------------------------------------------------------------------------------