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

.Rbuildignore

.gitIgnore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

DESCRIPTION

NAMESPACE

R/annotateOfftargets.R R/buildFeatureVectorForScoring.R R/buildFeatureVectorForScoring2.R R/buildFeatureVectorForScoringBulge.R R/calculategRNAEfficiency.R R/calculategRNAEfficiency2.R R/calculategRNAEfficiencyCRISPRscan.R R/compare2Sequences.R R/deepCpf1.R R/designPEs.R R/filterOffTarget.R R/filterOffTargetWithoutBSgenome.R R/filtergRNAs.R R/findgRNAs.R R/getExtendedSequence.R R/getOfftargetScore.R R/getOfftargetScore2.R R/getOfftargetScoreBulge.R R/getSeqFromBed.R R/isPatternUnique.R R/offTargetAnalysis.R R/offTargetAnalysisWithoutBSgenome.R R/predictRelativeFreqIndels.R R/searchHits.R R/searchHits2.R R/translatePattern.R R/uniqueREs.R R/writeHits.R R/writeHits2.R README.Rmd README.md

inst/CITATION

inst/NEWS

inst/extdata/CRISPRscanEff.RDS

inst/extdata/Cpf1Eff.RDS

inst/extdata/DeepCpf1/real_weights/DeepCpf1_weights.h5

inst/extdata/DeepCpf1/real_weights/Seq_deepCpf1_weights.h5

inst/extdata/DoenchNBT2014.csv

inst/extdata/ForTestinguniqueREs.RData

inst/extdata/Lindel/Predictor.py

inst/extdata/Lindel/RLindelprediction.py

inst/extdata/Lindel/model_prereq.pkl

inst/extdata/Lindel/model_weights1.h5

inst/extdata/Lindel/model_weights2.h5

inst/extdata/Lindel/model_weights3_1.h5

inst/extdata/Lindel/model_weights3_2.h5

inst/extdata/Lindel/model_weights4.h5

inst/extdata/Lindel/model_weights5.h5

inst/extdata/Lindel/model_weights6.h5

inst/extdata/Morenos-Mateo.csv

inst/extdata/NEBenzymes.fa

inst/extdata/NatureBiot2016SuppTable19DoenchRoot.csv

inst/extdata/NatureBiot2016SuppTable19DoenchRoot.xlsx

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/all.gRNAs.df.RDS

inst/extdata/cpf1-2.fa

inst/extdata/cpf1.fa

inst/extdata/featureVecorsWithNinPAM.RDS

inst/extdata/foldgRNAs.R

inst/extdata/foldgRNAs.Rd

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/REcutDetails.xls

inst/extdata/gRNAProvidedSearchNOoffTarget/Summary.xls

inst/extdata/gRNAProvidedSearchNOoffTarget/gRNAsCRISPRseek.bed

inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/OfftargetAnalysis.xls

inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/REcutDetails.xls

inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/Summary.xls

inst/extdata/gRNAProvidedSearchNOoffTargetNoAnn/gRNAsCRISPRseek.bed

inst/extdata/gRNAsCpf1.RDS

inst/extdata/gRNAsSpCas9.RDS

inst/extdata/genomeSeq.fasta

inst/extdata/hits.txt

inst/extdata/input_example.txt

inst/extdata/input_example2.txt

inst/extdata/inputseq.fa

inst/extdata/inputseqWithoutBSgenome.fa

inst/extdata/kerasInstallation.txt

inst/extdata/output_example.txt

inst/extdata/output_example2.txt

inst/extdata/pairedSearch/withRE/Hsap_GATA1_ex2.gbk

inst/extdata/pairedSearch/withRE/OfftargetAnalysis.xls

inst/extdata/pairedSearch/withRE/REcutDetails.xls

inst/extdata/pairedSearch/withRE/Summary.xls

inst/extdata/pairedSearch/withRE/gRNAsCRISPRseek.bed

inst/extdata/pairedSearch/withRE/inputseqallgRNAs.fa

inst/extdata/pairedSearch/withRE/pairedgRNAs.xls

inst/extdata/pairedSearch/withoutRE/Hsap_GATA1_ex2.gbk

inst/extdata/pairedSearch/withoutRE/OfftargetAnalysis.xls

inst/extdata/pairedSearch/withoutRE/REcutDetails.xls

inst/extdata/pairedSearch/withoutRE/Summary.xls

inst/extdata/pairedSearch/withoutRE/gRNAsCRISPRseek.bed

inst/extdata/pairedSearch/withoutRE/inputseqallgRNAs.fa

inst/extdata/pairedSearch/withoutRE/pairedgRNAs.xls

inst/extdata/python/DeepCpf1.py

inst/extdata/python/input_example.txt

inst/extdata/python/input_example2.txt

inst/extdata/python/kerasInstallation.txt

inst/extdata/python/output_example.txt

inst/extdata/python/output_example2.txt

inst/extdata/python/readme

inst/extdata/python/weights/DeepCpf1_weights.h5

inst/extdata/python/weights/Seq_deepCpf1_weights.h5

inst/extdata/readme

inst/extdata/real_weights/DeepCpf1_weights.h5

inst/extdata/real_weights/Seq_deepCpf1_weights.h5

inst/extdata/recreateTestResults.R

inst/extdata/rs362331C.fa

inst/extdata/rs362331T.fa

inst/extdata/runUnitTestOneByOne.txt

inst/extdata/seqs2.5prime.RDS

inst/extdata/seqs2.RDS

inst/extdata/seqs2CFD.RDS

inst/extdata/test.bed

inst/extdata/testCRISPRscan.fa

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/gRNAsCRISPRseek.bed

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/gRNAsCRISPRseek.bed

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/gRNAsCRISPRseek.bed

inst/extdata/testMouse/WithorgAnn/mRIPK1stop.gbk

inst/extdata/testMouse/WithorgAnn/pairedgRNAs.xls

inst/extdata/testNoTarget/OfftargetAnalysis.xls

inst/extdata/testNoTarget/REcutDetails.xls

inst/extdata/testNoTarget/Summary.xls

inst/extdata/testNoTarget/negativeCntl-gRNA.fa

inst/extdata/testSeqForDeepCpf1.RDS

inst/extdata/testspeed.fa

inst/extdata/tobi2.fa

inst/extdata/unPairedSearch/withRE/Hsap_GATA1_ex2.gbk

inst/extdata/unPairedSearch/withRE/OfftargetAnalysis.xls

inst/extdata/unPairedSearch/withRE/REcutDetails.xls

inst/extdata/unPairedSearch/withRE/Summary.xls

inst/extdata/unPairedSearch/withRE/gRNAsCRISPRseek.bed

inst/extdata/unPairedSearch/withRE/inputseqallgRNAs.fa

inst/extdata/unPairedSearch/withRE/pairedgRNAs.xls

inst/extdata/unPairedSearch/withoutRE/Hsap_GATA1_ex2.gbk

inst/extdata/unPairedSearch/withoutRE/OfftargetAnalysis.xls

inst/extdata/unPairedSearch/withoutRE/REcutDetails.xls

inst/extdata/unPairedSearch/withoutRE/Summary.xls

inst/extdata/unPairedSearch/withoutRE/gRNAsCRISPRseek.bed

inst/extdata/unPairedSearch/withoutRE/inputseqallgRNAs.fa

inst/extdata/unPairedSearch/withoutRE/pairedgRNAs.xls

inst/extdata/weights/DeepCpf1_weights.h5

inst/extdata/weights/Seq_deepCpf1_weights.h5

tests/.DS_Store

tests/runTests.R tests/testthat.R tests/testthat/test-compare2Sequences.R tests/testthat/test-deepCpf1.R tests/testthat/test-findgRNAs.R tests/testthat/test-gRNAprovidedCompare2Seqs.R tests/testthat/test-gRNAprovidedNoPAM.R tests/testthat/test-getOfftargetScore2.R tests/testthat/test-mouse_orgAnn_annotateExon.R tests/testthat/test-offTargetAnalysis.R tests/testthat/test-targetNotFound.R tests/testthat/test-targetOffNotFound.R tests/testthat/test-targetOffNotFound_5prime.R

vignettes/CRISPRseek.Rnw

LihuaJulieZhu/CRISPRseek documentation built on Feb. 3, 2024, 2:44 p.m.

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

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

R Package Documentation

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

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

R Package Documentation

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We want your feedback!

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

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