Index

B

build_counts_anndata() (screenpro.ngs.GuideCounter method)

buildPhenotypeData() (screenpro.assays.PooledScreens method)

C

calculateDelta() (in module screenpro.phenoscore.delta) calculateDrugScreen() (screenpro.assays.PooledScreens method) calculateDrugScreenDESeq() (screenpro.assays.PooledScreens method) calculateFlowBasedScreen() (screenpro.assays.PooledScreens method)

compareByReplicates() (in module screenpro.phenoscore.delta) compareByTargetGroup() (in module screenpro.phenoscore.delta) copy() (screenpro.assays.PooledScreens method) countNormalization() (screenpro.assays.PooledScreens method)

D

DataDashboard (class in screenpro.dashboard)

drawVolcano() (screenpro.assays.PooledScreens method) DrugScreenDashboard (class in screenpro.dashboard)

F

fastq_to_count_dual_guide() (in module screenpro.ngs.cas9)

fastq_to_count_single_guide() (in module screenpro.ngs.cas9) filterLowCounts() (screenpro.assays.PooledScreens method)

G

GammaVolcanoPlot() (screenpro.dashboard.DrugScreenDashboard method) generatePseudoGeneAnnData() (in module screenpro.phenoscore.delta) get_counts_matrix() (screenpro.ngs.GuideCounter method) getBestTargetByTSS() (in module screenpro.phenoscore.delta)

getPhenotypeData() (in module screenpro.phenoscore.delta) getPhenotypeScores() (screenpro.assays.PooledScreens method) GImaps (class in screenpro.assays) GuideCounter (class in screenpro.ngs)

L

label_as_black() (in module screenpro.plotting.pheno_plots) label_by_color() (in module screenpro.plotting.pheno_plots) label_resistance_hit() (in module screenpro.plotting.pheno_plots) label_sensitivity_hit() (in module screenpro.plotting.pheno_plots)

listPhenotypeScores() (screenpro.assays.PooledScreens method) load_cas9_sgRNA_library() (in module screenpro.load) load_counts_matrix() (screenpro.ngs.GuideCounter method) load_library() (screenpro.ngs.GuideCounter method) loadScreenProcessingData() (in module screenpro.load)

M

map_to_library_dual_guide() (in module screenpro.ngs.cas9) map_to_library_single_guide() (in module screenpro.ngs.cas9) matrixStat() (in module screenpro.phenoscore.phenostat) module screenpro.assays screenpro.dashboard screenpro.load screenpro.ngs screenpro.ngs.cas12 screenpro.ngs.cas9 screenpro.phenoscore screenpro.phenoscore.delta screenpro.phenoscore.deseq screenpro.phenoscore.phenostat screenpro.plotting.pheno_plots screenpro.plotting.qc_plots

multipleTestsCorrection() (in module screenpro.phenoscore.phenostat)

P

plotCountDistribution() (in module screenpro.plotting.qc_plots)

plotReplicateScatter() (in module screenpro.plotting.qc_plots) PooledScreens (class in screenpro.assays)

R

RhoGammaScatter() (screenpro.dashboard.DrugScreenDashboard method)

RhoVolcanoPlot() (screenpro.dashboard.DrugScreenDashboard method) runPhenoScore() (in module screenpro.phenoscore)

S

screenpro.assays module screenpro.dashboard module screenpro.load module screenpro.ngs module screenpro.ngs.cas12 module screenpro.ngs.cas9 module

screenpro.phenoscore module screenpro.phenoscore.delta module screenpro.phenoscore.deseq module screenpro.phenoscore.phenostat module screenpro.plotting.pheno_plots module screenpro.plotting.qc_plots module

V

volcano_plot() (in module screenpro.plotting.pheno_plots)