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.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.compareContrasts     Identify Replicated Signals in Pooled Screens
                        Using Conditional Scoring
ct.contrastBarchart     Visualize Signal Across A List of Contrasts
ct.expandAnnotation     Expand an annotation object to allow
                        annotations of reagents to multiple targets
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.keyCheck             Check compatibility of a sample key with a
                        supplied ExpressionSet or similar 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.normalizeBySlope     Normalize sample abundance estimates by the
                        slope of the values in the central range
ct.normalizeFQ          Apply Factored Quantile Normalization to an
                        eset
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 specific shared elements
ct.parseGeneSymbol      Parse 'geneSymbol' values to construct an
                        alternative annotation list
ct.prepareAnnotation    Check and optionally subset an annotation file
                        for use in a Crispr Screen
ct.rankSimple           Rank Signals in a Simplified Pooled Screen
                        Result Object
ct.rawCountDensities    Visualization of Raw gRNA Count Densities
ct.regularizeContrasts
                        Regularize Two Screening Results Objects
ct.resultCheck          Determine whether a supplied object contains
                        the results of a Pooled Screen
ct.scatter              Compare Two CRISPR Screen Contrasts via a
                        Scatter Plot
ct.seas                 Geneset Enrichment within a CRISPR screen using
                        'sparrow'
ct.seasPrep             Prepare one or more resultsDF objects for
                        analysis via Sparrow.
ct.signalSummary        Generate a Figure Summarizing Overall Signal
                        for One or More Targets
ct.simpleResult         Convert a verbose results DF object to a
                        gene-level result object
ct.softLog              Log10 transform empirical P-values with a
                        pseudocount
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.topTargets           Display the log2 fold change estimates and
                        associated standard deviations of the guides
                        targeting the top candidates in a crispr screen
ct.upSet                Consolidate shared signals across many
                        contrasts in an UpSet Plot
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
