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...
CorrViewVisualize the correlation between two object
countsummaryCount summary data generated by running MAGeCK count
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
EnrichedGeneViewVisualize selected genes in enriched genesets
EnrichedGSEViewView enriched terms in GSEA
EnrichedViewView enriched terms
enrich.GSEGSEA
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.
HeatmapViewDraw heatmap
IdentBarViewIdentical bar plot
KeggPathwayViewKegg pathway view
MapRatesViewView mapping ratio
MAViewMAplot of gene beta scores
mle.gene_summaryGene summary table in MAGeCK MLE results
noEnrichPlotBlank figure
NormalizeBetaNormalize gene beta scores
normalize.loessnormalize.loess
RankViewView the rank of gene points
ReadBetaRead gene beta scores
readGMTReadGMT
ReadRRARead gene summary file in MAGeCK-RRA results
ReadsgRRARead sgRNA summary in MAGeCK-RRA results
rra.gene_summaryGene summary data generated by running MAGeCK RRA
rra.sgrna_summarysgRNA summary data generated by running MAGeCK RRA
ScatterViewScatter plot
SelectorSelect signatures from candidate list (according to the...
sgRankViewView the rank of sgRNA points in horizontal bars.
SquareViewScatter plot of 9-Square
TransGeneIDGene ID conversion between ENTREZID and SYMBOL
ViolinViewViolin plot
VolcanoViewVolcano View
Zuber_EssentialCore essential gene list
MAGeCKFlute documentation built on Dec. 10, 2018, 6 p.m.