├── .BBSoptions ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── data.R ├── getCFDScores.R ├── getCRISPRscanScores.R ├── getCasRxRFScores.R ├── getCrispraterScores.R ├── getDeepHFScores.R ├── getEnPAMGBScores.R ├── getLindelScores.R ├── getMITScores.R ├── getRuleSet1Scores.R ├── getRuleSet3Scores.R ├── sysdata.rda ├── utils.R └── zzz.R ├── README.Rmd ├── README.md ├── data ├── datalist └── scoringMethodsInfo.rda ├── inst ├── CITATION ├── NEWS.Rd ├── casrxrf │ ├── Cas13designGuidePredictorInput.csv.gz │ ├── LICENSE.txt │ ├── LocalNTdensityCorrelations.txt │ ├── RNAhyb.sh │ ├── binaryInstall.sh │ ├── changes.txt │ └── test.fa ├── cfd_cas9 │ ├── cfd.mm.scores.cas9.rda │ ├── cfd.mm.scores.cas9.txt │ ├── cfd.mm.weights.cas9.rda │ ├── cfd.pam.scores.cas9.rda │ ├── cfd.pam.scores.cas9.txt │ ├── cfd.pam.weights.cas9.rda │ └── process.R ├── cfd_casrx │ ├── CasRxWeights.csv │ ├── cfd.mm.weights.casrx.rda │ ├── cfd.pam.weights.casrx.rda │ └── process.R ├── createSysdata.R ├── crisprscan │ ├── 41592_2015_BFnmeth3543_MOESM640_ESM.xlsx │ ├── crisprscan_coefficients.csv │ ├── readme.txt │ └── reformat.R ├── mit │ ├── mit.jpg │ ├── mit.weights.rda │ ├── mit.weights.txt │ └── processWeights.R ├── python │ ├── buildingCondaEnvironments.sh │ ├── deephf-env.yml │ ├── deephf │ │ ├── changes.txt │ │ ├── deephf │ │ │ ├── README.md │ │ │ ├── feature_util.py │ │ │ ├── prediction_util.py │ │ │ ├── sequences.txt │ │ │ └── training_util.py │ │ ├── getDeepHF.py │ │ ├── setup.cfg │ │ └── setup.py │ ├── downloads.txt │ ├── enpamgb-env.yml │ ├── enpamgb │ │ ├── AUTHORS.rst │ │ ├── CONTRIBUTING.rst │ │ ├── HISTORY.rst │ │ ├── LICENSE │ │ ├── README.rst │ │ ├── changes.txt │ │ ├── docs │ │ │ ├── Makefile │ │ │ ├── authors.rst │ │ │ ├── conf.py │ │ │ ├── contributing.rst │ │ │ ├── history.rst │ │ │ ├── index.rst │ │ │ ├── installation.rst │ │ │ ├── make.bat │ │ │ ├── modules.rst │ │ │ ├── readme.rst │ │ │ ├── requirements.txt │ │ │ ├── sgrna_modeler.rst │ │ │ └── usage.rst │ │ ├── getEnPAMGB.py │ │ ├── setup.py │ │ ├── sgrna_modeler │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ │ ├── features │ │ │ │ │ └── physiochem.csv.zip │ │ │ │ └── saved_models │ │ │ │ │ ├── Seq_deepCpf1_weights_tf.h5 │ │ │ │ │ └── enPAM_GB.joblib │ │ │ ├── datasets.py │ │ │ ├── enzymes.py │ │ │ ├── features.py │ │ │ ├── models.py │ │ │ └── mutagenesis.py │ │ └── tests │ │ │ ├── test_data │ │ │ └── kim_2019_rs2_predictions.csv.zip │ │ │ └── test_sgrna_modeler.py │ ├── lindel-env.yml │ ├── lindel │ │ ├── LICENSE │ │ ├── Lindel │ │ │ ├── Predictor.py │ │ │ ├── __init__.py │ │ │ └── model_prereq.pkl │ │ ├── Lindel_prediction.py │ │ ├── MANIFEST.in │ │ ├── README.md │ │ ├── changes.txt │ │ ├── example.txt │ │ └── setup.py │ ├── rs3-env.yml │ └── rs3 │ │ ├── LICENSE │ │ ├── getRuleSet3ScoresSequence.py │ │ ├── predict.py │ │ ├── predicttarg.py │ │ ├── readme.txt │ │ ├── seq.py │ │ ├── sequences.txt │ │ ├── setup.sh │ │ ├── targetdata.py │ │ └── targetfeat.py ├── roster │ ├── methods.txt │ ├── processRoster.R │ └── roster.pptx └── ruleset1 │ └── coefficients.csv ├── longtests ├── testthat.R └── testthat │ └── test-ontargets.R ├── man ├── getCFDScores.Rd ├── getCRISPRaterScores.Rd ├── getCRISPRscanScores.Rd ├── getCasRxRFScores.Rd ├── getDeepHFScores.Rd ├── getEnPAMGBScores.Rd ├── getLindelScores.Rd ├── getMITScores.Rd ├── getRuleSet1Scores.Rd ├── getRuleSet3Scores.Rd └── scoringMethodsInfo.Rd ├── tests ├── testthat.R └── testthat │ ├── test-crisprscan.R │ ├── test-offtargets.R │ └── test-ruleset1.R └── vignettes ├── crisprScore.Rmd ├── figures ├── resave.sh ├── sequences_cas12a_v1.pdf ├── sequences_cas12a_v1.pptx ├── sequences_cas12a_v1.svg ├── sequences_cas12a_v2.pdf ├── sequences_cas12a_v2.pptx ├── sequences_cas12a_v2.svg ├── sequences_cas9_v1.pdf ├── sequences_cas9_v1.pptx ├── sequences_cas9_v1.svg ├── sequences_cas9_v2.pdf ├── sequences_cas9_v2.pptx └── sequences_cas9_v2.svg └── references.bib /.BBSoptions: 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