Files in CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
NAMESPACE
DESCRIPTION
R/predictRelativeFreqIndels.R
R/findgRNAs.R
R/compare2Sequences.R
R/filtergRNAs.R
R/getOfftargetScore.R
R/buildFeatureVectorForScoring2.R
R/offTargetAnalysis.R
R/calculategRNAEfficiency2.R
R/writeHits.R
R/getExtendedSequence.R
R/annotateOfftargets.R
R/filterOffTargetWithoutBSgenome.R
R/writeHits2.R
R/designPEs.R
R/offTargetAnalysisWithoutBSgenome.R
R/searchHits.R
R/calculategRNAEfficiencyCRISPRscan.R
R/getOfftargetScore2.R
R/buildFeatureVectorForScoring.R
R/filterOffTarget.R
R/searchHits2.R
R/uniqueREs.R
R/calculategRNAEfficiency.R
R/getSeqFromBed.R
R/translatePattern.R
R/isPatternUnique.R
inst/NEWS
inst/CITATION
inst/doc/CRISPRseek.Rnw
inst/doc/CRISPRseek.pdf
inst/doc/CRISPRseek.R
inst/extdata/tobi2.fa
inst/extdata/hits.txt
inst/extdata/NEBenzymes.fa
inst/extdata/seqs2CFD.RData
inst/extdata/T2plus100OffTargets.bed
inst/extdata/rs362331T.fa
inst/extdata/seqs2.RData
inst/extdata/rs362331C.fa
inst/extdata/cpf1.fa
inst/extdata/NatureBiot2016SuppTable19DoenchRoot.csv
inst/extdata/genomeSeq.fasta
inst/extdata/Morenos-Mateo.csv
inst/extdata/foldgRNAs.R
inst/extdata/T2.fa
inst/extdata/test.bed
inst/extdata/testspeed.fa
inst/extdata/ForTestinguniqueREs.RData
inst/extdata/RIPK1stop.fa
inst/extdata/testCRISPRscan.fa
inst/extdata/inputseqWithoutBSgenome.fa
inst/extdata/inputseq.fa
inst/extdata/foldgRNAs.Rd
inst/extdata/seqs2.5prime.RData
inst/extdata/DoenchNBT2014.csv
inst/extdata/testHsap_GATA1_ex2_gRNA1.fa
inst/extdata/recreateTestResults.R
inst/extdata/testMouse/NOorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/NOorgAnn/pairedgRNAs.xls
inst/extdata/testMouse/NOorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOorgAnn/REcutDetails.xls
inst/extdata/testMouse/NOorgAnn/Summary.xls
inst/extdata/testMouse/NOorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/WithorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls
inst/extdata/testMouse/WithorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/WithorgAnn/REcutDetails.xls
inst/extdata/testMouse/WithorgAnn/Summary.xls
inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/NOTannotateExon/OfftargetAnalysis.xls
inst/extdata/testMouse/NOTannotateExon/pairedgRNAs.xls
inst/extdata/testMouse/NOTannotateExon/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOTannotateExon/REcutDetails.xls
inst/extdata/testMouse/NOTannotateExon/Summary.xls
inst/extdata/testMouse/NOTannotateExon/mRIPK1stop.gbk
inst/extdata/testNoTarget/OfftargetAnalysis.xls
inst/extdata/testNoTarget/negativeCntl-gRNA.fa
inst/extdata/testNoTarget/Summary.xls
inst/extdata/Rule_Set_2_scoring_v1/README_v1.pdf
inst/extdata/Rule_Set_2_scoring_v1/analysis/X
inst/extdata/Rule_Set_2_scoring_v1/analysis/model_comparison.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/load_data.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/util.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/model_comparison.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/util.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/load_data.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/metrics.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/rs2_score_calculator.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/local_multiprocessing.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/predict.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/predict.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/local_multiprocessing.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/testfile
inst/extdata/Rule_Set_2_scoring_v1/analysis/temp
inst/extdata/Rule_Set_2_scoring_v1/analysis/metrics.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/baselines.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ensembles.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/GP.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/DNN.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/DNN.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/__init__.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/__init__.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/gpy_ssk.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/regression.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ensembles.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ssk.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/regression.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/featurization.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/featurization.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/microhomology.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/microhomology.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/__init__.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/__init__.py
inst/extdata/Rule_Set_2_scoring_v1/saved_models/V3_model_nopos.pickle
inst/extdata/Rule_Set_2_scoring_v1/saved_models/V3_model_full.pickle
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/gRNAsCRISPRseek.bed
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/REcutDetails.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/Summary.xls
inst/extdata/DeepCpf1/DeepCpf1.py
inst/extdata/DeepCpf1/kerasInstallation.txt
inst/extdata/DeepCpf1/input_example.txt
inst/extdata/DeepCpf1/output_example2.txt
inst/extdata/DeepCpf1/readme
inst/extdata/DeepCpf1/output_example.txt
inst/extdata/DeepCpf1/input_example2.txt
inst/extdata/DeepCpf1/weights/Seq_deepCpf1_weights.h5
inst/extdata/DeepCpf1/weights/DeepCpf1_weights.h5
inst/extdata/Lindel/model_weights3_2.h5
inst/extdata/Lindel/model_prereq.pkl
inst/extdata/Lindel/RLindelprediction.py
inst/extdata/Lindel/model_weights5.h5
inst/extdata/Lindel/model_weights2.h5
inst/extdata/Lindel/model_weights1.h5
inst/extdata/Lindel/model_weights4.h5
inst/extdata/Lindel/model_weights6.h5
inst/extdata/Lindel/Predictor.py
inst/extdata/Lindel/model_weights3_1.h5
inst/extdata/gRNAProvidedSearch/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearch/gRNAsCRISPRseek.bed
inst/extdata/gRNAProvidedSearch/REcutDetails.xls
inst/extdata/gRNAProvidedSearch/Summary.xls
inst/extdata/gRNAProvidedSearchNOoffTarget/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls
inst/extdata/pairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withRE/pairedgRNAs.xls
inst/extdata/pairedSearch/withRE/REcutDetails.xls
inst/extdata/pairedSearch/withRE/Summary.xls
inst/extdata/pairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls
inst/extdata/pairedSearch/withoutRE/REcutDetails.xls
inst/extdata/pairedSearch/withoutRE/Summary.xls
inst/extdata/unPairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls
inst/extdata/unPairedSearch/withRE/REcutDetails.xls
inst/extdata/unPairedSearch/withRE/Summary.xls
inst/extdata/unPairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls
inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls
inst/extdata/unPairedSearch/withoutRE/Summary.xls
inst/unitTests/test_getOfftargetScore2.R
inst/unitTests/test_compare2Sequences.R
inst/unitTests/test_mouse_orgAnn_annotateExon.R
inst/unitTests/test_gRNAprovidedNoPAM.R
inst/unitTests/test_targetNotFound.R
inst/unitTests/test_gRNAprovidedCompare2Seqs.R
inst/unitTests/test_offTargetAnalysis.R
build/vignette.rds
tests/runTests.R
vignettes/CRISPRseek.Rnw
man/predictRelativeFreqIndels.Rd
man/buildFeatureVectorForScoring.Rd
man/filtergRNA.Rd
man/writeHits.Rd
man/searchHits.Rd
man/CRISPRseek-package.Rd
man/filterOffTarget.Rd
man/annotateOffTargets.Rd
man/calculategRNAEfficiency.Rd
man/uniqueREs.Rd
man/findgRNAs.Rd
man/getOfftargetScore.Rd
man/compare2Sequences.Rd
man/writeHits2.Rd
man/searchHits2.Rd
man/isPatternUnique.Rd
man/offTargetAnalysisWithoutBSgenome.Rd
man/translatePattern.Rd
man/offTargetAnalysis.Rd
