Suite of Functions for Pooled Crispr Screen QC and Analysis

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Documentation for package ‘gCrisprTools’ version 2.13.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.buildSE	Package Screen Data into a 'SummarizedExperiment' Object
ct.CAT	Compare Two CRISPR Screens via a CAT plot
ct.compareContrasts	Identify Replicated Signals in Pooled Screens Using Conditional Scoring
ct.contrastBarchart	Visualize Signal Across A List of Contrasts
ct.DirectionalTests	Compute Directional P-values from eBayes Output
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.GCbias	Visualization of gRNA GC Content Trends
ct.generateResults	Calculate results of a crispr screen from a contrast
ct.GREATdb	Update a gene-centric msdb object for GREAT-style enrichment analysis using a specified CRISPR annotation.
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.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.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.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.ROC	Generate a Receiver-Operator Characteristic (ROC) Curve from a CRISPR 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
resultsDF	Precalculated gene-level summary of a crispr screen