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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.buildSE | Package Screen Data into a 'SummarizedExperiment' Object |
| ct.CAT | Compare Two CRISPR Screens via a CAT plot |
| 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.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.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.multiGSEA | Geneset Enrichment within a CRISPR screen using multiGSEA This function identifies differentially enriched/depleted ontological categories within the hits of a CRISPR screen given a provided 'GenseSetDb()' and a results 'data.frame' created by 'ct.generateResults()'. Testing is performed using a Hypergeometric test, and results are returned as a 'MultiGSEAResult' object defined in the 'multiGSEA' package. Note that the '@logFC' slot in the returned object will contain the median gRNA lfc across all associated guides, which in some cases may have dubious interpretive value. This method used overrepresentation analysis, derived from 'limma::kegga()', and incorporates the number of gRNAs associated with each Target (inferred from the 'geneSymbol' column of the 'resultsDF') as the bias vector (because standard aggregation methods should be underpowered for targets with few guides). Setting 'unbiased' = 'TRUE' suppresses this behavior, which is identical to a hypergeometric test. |
| ct.normalizeBySlope | Normalize sample abundance estimates by the slope of the values in the central range |
| ct.normalizeFactoredQuantiles | Apply Factored Quantile Normalization to gRNA counts |
| ct.normalizeFQ | Factored Quantile Normalization |
| 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.signalSummary | Generate a Figure Summarizing Overall Signal for One or More Targets |
| 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 |