aln                     Precalculated alignment statistics of a crispr
                        screen
ann                     Annotation file for a mouse Crispr library
ct.CAT                  Compare Two CRISPR Screens via a CAT plot
ct.DirectionalTests     Compute Directional P-values from eBayes Output
ct.GCbias               Visualization of gRNA GC Content Trends
ct.GREATdb              Update a gene-centric msdb object for
                        GREAT-style enrichment analysis using a
                        specified CRISPR annotation.
ct.PRC                  Generate a Precision-Recall Curve from a CRISPR
                        screen
ct.PantherPathwayEnrichment
                        Run a (limited) Pathway Enrichment Analysis on
                        the results of a Crispr experiment.
ct.ROC                  Generate a Receiver-Operator Characteristic
                        (ROC) Curve from a CRISPR screen
ct.alignmentChart       View a Barchart Summarizing Alignment
                        Statistics for a Crispr Screen
ct.applyAlpha           Apply RRA 'alpha' cutoff to RRAalpha input
ct.buildSE              Package Screen Data into a
                        'SummarizedExperiment' Object
ct.filterReads          Remove low-abundance elements from an
                        ExpressionSet object
ct.gRNARankByReplicate
                        Visualization of Ranked gRNA Abundances by
                        Replicate
ct.generateResults      Calculate results of a crispr screen from a
                        contrast
ct.guideCDF             View CDFs of the ranked gRNAs or Targets
                        present in a crispr screen
ct.inputCheck           Check compatibility of a sample key with a
                        supplied object
ct.makeContrastReport   Generate a Contrast report from a pooled CRISPR
                        screen
ct.makeQCReport         Generate a QC report from a pooled CRISPR
                        screen
ct.makeReport           Generate a full experimental report from a
                        pooled CRISPR screen
ct.makeRhoNull          Make null distribution for RRAalpha tests
ct.multiGSEA            Geneset Enrichment within a CRISPR screen using
                        multiGSEA This function identifies
                        differentially enriched/depleted ontological
                        categories within the hits of a CRISPR screen
                        given a provided 'GenseSetDb()' and a results
                        'data.frame' created by 'ct.generateResults()'.
                        Testing is performed using a Hypergeometric
                        test, and results are returned as a
                        'MultiGSEAResult' object defined in the
                        'multiGSEA' package. Note that the '@logFC'
                        slot in the returned object will contain the
                        median gRNA lfc across all associated guides,
                        which in some cases may have dubious
                        interpretive value. This method used
                        overrepresentation analysis, derived from
                        'limma::kegga()', and incorporates the number
                        of gRNAs associated with each Target (inferred
                        from the 'geneSymbol' column of the
                        'resultsDF') as the bias vector (because
                        standard aggregation methods should be
                        underpowered for targets with few guides).
                        Setting 'unbiased' = 'TRUE' suppresses this
                        behavior, which is identical to a
                        hypergeometric test.
ct.normalizeBySlope     Normalize sample abundance estimates by the
                        slope of the values in the central range
ct.normalizeFQ          Factored Quantile Normalization
ct.normalizeFactoredQuantiles
                        Apply Factored Quantile Normalization to gRNA
                        counts
ct.normalizeGuides      Normalize an ExpressionSet Containing a Crispr
                        Screen
ct.normalizeMedians     Normalize sample abundance estimates by median
                        gRNA counts
ct.normalizeNTC         Normalize sample abundance estimates by the
                        median values of nontargeting control guides
ct.normalizeSpline      Normalize sample abundance estimates by a
                        spline fit to the nontargeting controls
ct.prepareAnnotation    Check and optionally subset an annotation file
                        for use in a Crispr Screen
ct.rawCountDensities    Visualization of Raw gRNA Count Densities
ct.resultCheck          Determine whether a supplied object contains
                        the results of a Pooled Screen
ct.signalSummary        Generate a Figure Summarizing Overall Signal
                        for One or More Targets
ct.stackGuides          View a stacked representation of the most
                        variable targets or individual guides within an
                        experiment, as a percentage of the total
                        aligned reads
ct.targetSetEnrichment
                        Test Whether a Specified Target Set is Enriched
                        Within a Pooled Screen
ct.topTargets           Display the log2 fold change estimates and
                        associated standard deviations of the guides
                        targeting the top candidates in a crispr screen
ct.viewControls         View nontargeting guides within an experiment
ct.viewGuides           Generate a Plot of individual gRNA Pair Data in
                        a Crispr Screen
es                      ExpressionSet of count data from a Crispr
                        screen with strong selection
essential.genes         Artificial list of 'essential' genes in the
                        example Crispr screen included for plotting
                        purposes
fit                     Precalculated contrast fit from a Crispr screen
gCrisprTools-package    gCrisprTools
resultsDF               Precalculated gene-level summary of a crispr
                        screen
