# Suite of Functions for Pooled Crispr Screen QC and Analysis

## Documentation for package ‘gCrisprTools’ version 1.4.0

- 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.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