Files in LihuaJulieZhu/CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

DESCRIPTION
NAMESPACE
R/annotateOfftargets.R R/buildFeatureVectorForScoring.R R/buildFeatureVectorForScoring2.R R/calculategRNAEfficiency.R R/calculategRNAEfficiency2.R R/compare2Sequences.R R/filterOffTarget.R R/filtergRNAs.R R/findgRNAs.R R/foldgRNAs.R R/getOfftargetScore.R R/getOfftargetScore2.R R/getSeqFromBed.R R/isPatternUnique.R R/offTargetAnalysis.R R/searchHits.R R/searchHits2.R R/translatePattern.R R/uniqueREs.R R/writeHits.R R/writeHits2.R
inst/CITATION
inst/NEWS
inst/extdata/DoenchNBT2014.csv
inst/extdata/ForTestinguniqueREs.RData
inst/extdata/NEBenzymes.fa
inst/extdata/NatureBiot2016SuppTable19DoenchRoot.csv
inst/extdata/RIPK1stop.fa
inst/extdata/Rule_Set_2_scoring_v1/.DS_Store
inst/extdata/Rule_Set_2_scoring_v1/README_v1.pdf
inst/extdata/Rule_Set_2_scoring_v1/analysis/.DS_Store
inst/extdata/Rule_Set_2_scoring_v1/analysis/X
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/__init__.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/__init__.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/featurization.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/features/featurization.pyc
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/load_data.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/load_data.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/local_multiprocessing.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/local_multiprocessing.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/metrics.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/metrics.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/model_comparison.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/model_comparison.pyc
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/GP.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/__init__.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/__init__.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/baselines.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ensembles.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ensembles.pyc
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/regression.pyc
inst/extdata/Rule_Set_2_scoring_v1/analysis/models/ssk.py
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/rs2_score_calculator.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/temp
inst/extdata/Rule_Set_2_scoring_v1/analysis/testfile
inst/extdata/Rule_Set_2_scoring_v1/analysis/util.py
inst/extdata/Rule_Set_2_scoring_v1/analysis/util.pyc
inst/extdata/Rule_Set_2_scoring_v1/saved_models/V3_model_full.pickle
inst/extdata/Rule_Set_2_scoring_v1/saved_models/V3_model_nopos.pickle
inst/extdata/T2.fa
inst/extdata/T2plus100OffTargets.bed
inst/extdata/cpf1.fa
inst/extdata/gRNAProvidedSearch/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearch/REcutDetails.xls
inst/extdata/gRNAProvidedSearch/Summary.xls
inst/extdata/gRNAProvidedSearch/gRNAsCRISPRseek.bed
inst/extdata/gRNAProvidedSearchNOoffTarget/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/OfftargetAnalysis.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/REcutDetails.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/Summary.xls
inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/gRNAsCRISPRseek.bed
inst/extdata/hits.txt
inst/extdata/inputseq.fa
inst/extdata/pairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withRE/REcutDetails.xls
inst/extdata/pairedSearch/withRE/Summary.xls
inst/extdata/pairedSearch/withRE/pairedgRNAs.xls
inst/extdata/pairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/pairedSearch/withoutRE/REcutDetails.xls
inst/extdata/pairedSearch/withoutRE/Summary.xls
inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls
inst/extdata/recreateTestResults.R
inst/extdata/rs362331C.fa
inst/extdata/rs362331T.fa
inst/extdata/seqs2.5prime.RData
inst/extdata/seqs2.RData
inst/extdata/seqs2CFD.RData
inst/extdata/test.bed
inst/extdata/testHsap_GATA1_ex2_gRNA1.fa
inst/extdata/testMouse/NOTannotateExon/OfftargetAnalysis.xls
inst/extdata/testMouse/NOTannotateExon/REcutDetails.xls
inst/extdata/testMouse/NOTannotateExon/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOTannotateExon/Summary.xls
inst/extdata/testMouse/NOTannotateExon/mRIPK1stop.gbk
inst/extdata/testMouse/NOTannotateExon/pairedgRNAs.xls
inst/extdata/testMouse/NOorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/NOorgAnn/REcutDetails.xls
inst/extdata/testMouse/NOorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/NOorgAnn/Summary.xls
inst/extdata/testMouse/NOorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/NOorgAnn/pairedgRNAs.xls
inst/extdata/testMouse/WithorgAnn/OfftargetAnalysis.xls
inst/extdata/testMouse/WithorgAnn/REcutDetails.xls
inst/extdata/testMouse/WithorgAnn/RIPK1stopallgRNAs.fa
inst/extdata/testMouse/WithorgAnn/Summary.xls
inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk
inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls
inst/extdata/testNoTarget/OfftargetAnalysis.xls
inst/extdata/testNoTarget/Summary.xls
inst/extdata/testNoTarget/negativeCntl-gRNA.fa
inst/extdata/testspeed.fa
inst/extdata/tobi2.fa
inst/extdata/unPairedSearch/withRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withRE/REcutDetails.xls
inst/extdata/unPairedSearch/withRE/Summary.xls
inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls
inst/extdata/unPairedSearch/withoutRE/OfftargetAnalysis.xls
inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls
inst/extdata/unPairedSearch/withoutRE/Summary.xls
inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls
inst/unitTests/test_compare2Sequences.R inst/unitTests/test_gRNAprovidedCompare2Seqs.R inst/unitTests/test_gRNAprovidedNoPAM.R inst/unitTests/test_getOfftargetScore2.R inst/unitTests/test_mouse_orgAnn_annotateExon.R inst/unitTests/test_offTargetAnalysis.R inst/unitTests/test_targetNotFound.R man/CRISPRseek-package.Rd man/annotateOffTargets.Rd man/buildFeatureVectorForScoring.Rd man/calculategRNAEfficiency.Rd man/compare2Sequences.Rd man/filterOffTarget.Rd man/filtergRNA.Rd man/findgRNAs.Rd man/foldgRNAs.Rd man/getOfftargetScore.Rd man/isPatternUnique.Rd man/offTargetAnalysis.Rd man/searchHits.Rd man/searchHits2.Rd man/translatePattern.Rd man/uniqueREs.Rd man/writeHits.Rd man/writeHits2.Rd tests/runTests.R
vignettes/CRISPRseek.Rnw
LihuaJulieZhu/CRISPRseek documentation built on Sept. 1, 2018, 8:50 a.m.