Man pages for MAGeCKFlute
Integrative analysis pipeline for pooled CRISPR functional genetic screens

arrangePathviewKegg pathway view and arrange grobs on page
BatchRemoveBatch effect removal
CellCycleViewEstimate cell cycle time for all samples compared to control...
CutoffCallingCall cutoff
DensityDiffViewDensity plot for beta score deviation between Control and...
DensityViewDensity plot for gene beta scores in Control and Treatment
EnrichABEnrichment analysis for Positive and Negative selection genes
enrich.DAVIDDo enrichment analysis using DAVID
EnrichedGSEViewView enriched terms in GSEA
EnrichedViewView enriched terms
enrich.GOstatsDo enrichment analysis using GOstats
enrich.HGTDo enrichment analysis using Hypergeometric test
enrichment_analysisEnrichment analysis
enrich.ORTDo enrichment analysis using over-representation test
EnrichSquareEnrichment analysis for selected treatment related genes
FluteMLEDownstream analysis based on MAGeCK-MLE result
FluteRRADownstream analysis based on MAGeCK-RRA result
getOrgDetermine the gene annotation package.
HeatmapViewCalculate the similarity between samples and plot heatmap
KeggPathwayViewKegg pathway view
loginfoLog message
MAViewMAplot of gene beta scores
MLE_DataGene summary table in MAGeCK MLE results
NormalizeBetaNormalize gene beta scores
RankViewView the rank of gene points
ReadBetaRead gene beta scores
ReadRRARead MAGeCK-RRA data
RRA_DataGene summary data generated by running MAGeCK RRA
ScatterViewScatter plot
SquareViewScatter plot of 9-Square
TransGeneIDGene ID conversion between ENTREZID and SYMBOL
ViolinViewViolin plot
Zuber_EssentialCore essential gene list
MAGeCKFlute documentation built on May 2, 2018, 4:25 a.m.