Suite of Functions for Pooled Crispr Screen QC and Analysis

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Documentation for package ‘gCrisprTools’ version 1.8.0

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gCrisprTools-package gCrisprTools
aln Precalculated alignment statistics of a crispr screen
ann Annotation file for a mouse Crispr library
ct.alignmentChart View a Barchart Summarizing Alignment Statistics for a Crispr Screen
ct.applyAlpha Apply RRA 'alpha' cutoff to RRAalpha input
ct.DirectionalTests Compute Directional P-values from eBayes Output
ct.filterReads Remove low-abundance elements from an ExpressionSet object
ct.GCbias Visualization of gRNA GC Content Trends
ct.generateResults Calculate results of a crispr screen from a contrast
ct.gRNARankByReplicate Visualization of Ranked gRNA Abundances by Replicate
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.PantherPathwayEnrichment Run a (limited) Pathway Enrichment Analysis on the results of a Crispr experiment.
ct.PRC Generate a Precision-Recall Curve from a CRISPR screen
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.ROC Generate a Receiver-Operator Characteristic (ROC) Curve from a CRISPR 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
resultsDF Precalculated gene-level summary of a crispr screen