Man pages for OscarBrock/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.buildSEPackage Screen Data into a 'SummarizedExperiment' Object
ct.CATCompare Two CRISPR Screens via a CAT plot
ct.compareContrastsIdentify Replicated Signals in Pooled Screens Using...
ct.contrastBarchartVisualize Signal Across A List of Contrasts
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.expandAnnotationExpand an annotation object to allow annotations of reagents...
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.GREATdbUpdate a gene-centric msdb object for GREAT-style enrichment...
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.keyCheckCheck compatibility of a sample key with a supplied...
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.normalizeFQApply Factored Quantile Normalization to an eset
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...
ct.numcoresChecks and Possibly Sets the Number of Cores to be Used in...
ct.parseGeneSymbolParse 'geneSymbol' values to construct an alternative...
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.rankSimpleRank Signals in a Simplified Pooled Screen Result Object
ct.rawCountDensitiesVisualization of Raw gRNA Count Densities
ct.regularizeContrastsRegularize Two Screening Results Objects
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.scatterCompare Two CRISPR Screen Contrasts via a Scatter Plot
ct.seasGeneset Enrichment within a CRISPR screen using 'sparrow'
ct.seasPrepPrepare one or more resultsDF objects for analysis via...
ct.signalSummaryGenerate a Figure Summarizing Overall Signal for One or More...
ct.simpleResultConvert a verbose results DF object to a gene-level result...
ct.softLogLog10 transform empirical P-values with a pseudocount
ct.stackGuidesView a stacked representation of the most variable targets or...
ct.targetSetEnrichmentRun a (limited) Pathway Enrichment Analysis on the results of...
ct.topTargetsDisplay the log2 fold change estimates and associated...
ct.upSetConsolidate shared signals across many contrasts in an UpSet...
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
OscarBrock/gCrisprTools documentation built on Oct. 25, 2022, 7:29 a.m.