| aln | Precalculated alignment statistics of a crispr screen |
| ann | Annotation file for a mouse Crispr library |
| appendDateAndExt | Add formatted timestamp and extension to a file name |
| ct.alignmentChart | View a Barchart Summarizing Alignment Statistics for a Crispr... |
| ct.alphaBeta | Aggregation of P-value Ranks using a Beta Distribution and... |
| 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... |
| ct.contrastBarchart | Visualize Signal Across A List of Contrasts |
| ct.DirectionalTests | Compute Directional P-values from eBayes Output |
| ct.drawColorLegend | Draw a density color legend. |
| ct.drawFlat | Draw a horizontal line of a specified color. |
| ct.ecdf | Generate a cumulative tally of reads by guide rank |
| ct.expandAnnotation | Expand an annotation object to allow annotations of reagents... |
| ct.exprsColor | Assign Colors Based on the Position of a Value in a... |
| 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... |
| ct.gRNARankByReplicate | Visualization of Ranked gRNA Abundances by Replicate |
| ct.guideCDF | View CDFs of the ranked gRNAs or Targets present in a crispr... |
| ct.inputCheck | Check compatibility of a sample key with a supplied object |
| ct.keyCheck | Check compatibility of a sample key with a supplied... |
| 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... |
| ct.makeRhoNull | Make null distribution for RRAalpha tests |
| ct.normalizeBySlope | Normalize sample abundance estimates by the slope of the... |
| 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... |
| ct.normalizeSpline | Normalize sample abundance estimates by a spline fit to... |
| ct.numcores | Checks and Possibly Sets the Number of Cores to be Used in... |
| ct.parseGeneSymbol | Parse 'geneSymbol' values to construct an alternative... |
| ct.PRC | Generate a Precision-Recall Curve from a CRISPR screen |
| ct.prepareAnnotation | Check and optionally subset an annotation file for use in a... |
| ct.preprocessFit | Preprocess a 'MArrayLM' model fit object to include only one... |
| 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... |
| ct.ROC | Generate a Receiver-Operator Characteristic (ROC) Curve from... |
| ct.RRAalpha | Aggregation of P-value Ranks using a Beta Distribution and... |
| ct.RRAalphaBatch | Create Batches of Null Permutations for a Crispr Screen |
| ct.RRAaPvals | gRNA signal aggregation via RRAa |
| 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... |
| ct.signalSummary | Generate a Figure Summarizing Overall Signal for One or More... |
| ct.simpleResult | Convert a verbose results DF object to a gene-level result... |
| ct.softLog | Log10 transform empirical P-values with a pseudocount |
| ct.stackGuides | View a stacked representation of the most variable targets or... |
| ct.targetSetEnrichment | Run a (limited) Pathway Enrichment Analysis on the results of... |
| ct.topTargets | Display the log2 fold change estimates and associated... |
| ct.upSet | Consolidate shared signals across many contrasts in an UpSet... |
| ct.viewControls | View nontargeting guides within an experiment |
| ct.viewGuides | Generate a Plot of individual gRNA Pair Data in a Crispr... |
| dir.writable | Checks that the directory provided is writable by the current... |
| es | ExpressionSet of count data from a Crispr screen with strong... |
| essential.genes | Artificial list of 'essential' genes in the example Crispr... |
| fit | Precalculated contrast fit from a Crispr screen |
| gCrisprTools-package | gCrisprTools |
| initOutDir | Initializes the output directory |
| renderReport | Internal wrapper to generate html markdown reports from... |
| resultsDF | Precalculated gene-level summary of a crispr screen |
