aln                     Precalculated alignment statistics of a crispr
                        screen
ann                     Annotation file for a mouse Crispr library
ct.DirectionalTests     Compute Directional P-values from eBayes Output
ct.GCbias               Visualization of gRNA GC Content Trends
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.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.normalizeBySlope     Normalize sample abundance estimates by the
                        slope of the values in the a central range
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.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
