# Suite of Functions for Pooled Crispr Screen QC and Analysis

## Documentation for package ‘gCrisprTools’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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