Man pages for gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and Analysis

alnPrecalculated alignment statistics of a crispr screen
annAnnotation file for a mouse Crispr library
appendDateAndExtAdd formatted timestamp and extension to a file name
ct.alignmentChartView a Barchart Summarizing Alignment Statistics for a Crispr...
ct.alphaBetaAggregation of P-value Ranks using a Beta Distribution and...
ct.applyAlphaApply RRA 'alpha' cutoff to RRAalpha input
ct.DirectionalTestsCompute Directional P-values from eBayes Output
ct.drawColorLegendDraw a density color legend.
ct.drawFlatDraw a horizontal line of a specified color.
ct.ecdfGenerate a cumulative tally of reads by guide rank
ct.exprsColorAssign Colors Based on the Position of a Value in a...
ct.filterReadsRemove low-abundance elements from an ExpressionSet object
ct.GCbiasVisualization of gRNA GC Content Trends
ct.generateResultsCalculate results of a crispr screen from a contrast
ct.getPantherExtract a Named List of Entrez IDs Annotated to Each Pathway...
ct.gRNARankByReplicateVisualization of Ranked gRNA Abundances by Replicate
ct.guideCDFView CDFs of the ranked gRNAs or Targets present in a crispr...
ct.inputCheckCheck compatibility of a sample key with a supplied object
ct.makeContrastReportGenerate a Contrast report from a pooled CRISPR screen
ct.makeQCReportGenerate a QC report from a pooled CRISPR screen
ct.makeReportGenerate a full experimental report from a pooled CRISPR...
ct.makeRhoNullMake null distribution for RRAalpha tests
ct.normalizeBySlopeNormalize sample abundance estimates by the slope of the...
ct.normalizeGuidesNormalize an ExpressionSet Containing a Crispr Screen
ct.normalizeMediansNormalize sample abundance estimates by median gRNA counts
ct.normalizeNTCNormalize sample abundance estimates by the median values of...
ct.normalizeSplineNormalize sample abundance estimates by a spline fit to the...
ct.numcoresChecks and Possibly Sets the Number of Cores to be Used in...
ct.PantherPathwayEnrichmentRun a (limited) Pathway Enrichment Analysis on the results of...
ct.PRCGenerate a Precision-Recall Curve from a CRISPR screen
ct.prepareAnnotationCheck and optionally subset an annotation file for use in a...
ct.preprocessFitPreprocess a "MArrayLM" model fit object to include only one...
ct.rawCountDensitiesVisualization of Raw gRNA Count Densities
ct.resultCheckDetermine whether a supplied object contains the results of a...
ct.ROCGenerate a Receiver-Operator Characteristic (ROC) Curve from...
ct.RRAalphaAggregation of P-value Ranks using a Beta Distribution and...
ct.RRAalphaBatchCreate Batches of Null Permutations for a Crispr Screen
ct.RRAaPvalsgRNA signal aggregation via RRAa
ct.stackGuidesView a stacked representation of the most variable targets or...
ct.targetSetEnrichmentTest Whether a Specified Target Set is Enriched Within a...
ct.topTargetsDisplay the log2 fold change estimates and associated...
ct.viewControlsView nontargeting guides within an experiment
ct.viewGuidesGenerate a Plot of individual gRNA Pair Data in a Crispr...
dir.writableChecks that the directory provided is writable by the current...
esExpressionSet of count data from a Crispr screen with strong...
essential.genesArtificial list of 'essential' genes in the example Crispr...
fitPrecalculated contrast fit from a Crispr screen
gCrisprTools-packagegCrisprTools
initOutDirInitializes the output directory
renderReportInternal wrapper to generate html markdown reports from...
resultsDFPrecalculated gene-level summary of a crispr screen
gCrisprTools documentation built on Nov. 17, 2017, 1:37 p.m.