Integrative analysis pipeline for pooled CRISPR functional genetic screens


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Documentation for package ‘MAGeCKFlute’ version 1.4.3

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arrangePathview Kegg pathway view and arrange grobs on page
BatchRemove Batch effect removal
CellCycleView Visualize the estimate cell cycle compared to control.
countsummary Count summary data generated by running MAGeCK count
CutoffCalling Quantile of normal distribution.
DensityDiffView Density plot
DensityView Density plot for gene beta scores in Control and Treatment
enrich.GSE Gene set enrichment analysis
enrich.HGT Do enrichment analysis using Hypergeometric test
enrich.ORT Do enrichment analysis using over-representation test
EnrichAB Enrichment analysis for Positive and Negative selection genes
EnrichAnalyzer Enrichment analysis
EnrichedFilter Simplify the enrichment results based on Jaccard index
EnrichedGeneView Visualize enriched pathways and genes in those pathways
EnrichedView View enriched terms
enrichGSE Gene set enrichment analysis
enrichment Enrichment analysis
enrichORT Do enrichment analysis using over-representation test
EnrichSquare Enrichment analysis for selected treatment related genes
FluteMLE Downstream analysis based on MAGeCK-MLE result
flutemle Downstream analysis based on MAGeCK-MLE result
FluteRRA Downstream analysis based on MAGeCK-RRA result
getOrg Determine the gene annotation package.
gsGetter Extract pathway annotation from GMT file.
HeatmapView Draw heatmap
Hypergeometric Do enrichment analysis using Hypergeometric test
IdentBarView Identical bar plot
KeggPathwayView Kegg pathway view
loess.normalize normalize.loess
MapRatesView View mapping ratio
MAView MAplot of gene beta scores
mle.gene_summary Gene summary table in MAGeCK MLE results
noEnrichPlot Blank figure
normalize.loess normalize.loess
NormalizeBeta Normalize gene beta scores
normalizebeta Normalize gene beta scores
RankView View the rank of gene points
rankview View the rank of gene points
ReadBeta Read gene beta scores
readbeta Read gene beta scores
ReadGMT ReadGMT
ReadRRA Read gene summary file in MAGeCK-RRA results
readrra Read gene summary file in MAGeCK-RRA results
ReadsgRRA Read sgRNA summary in MAGeCK-RRA results
rra.gene_summary Gene summary data generated by running MAGeCK RRA
rra.sgrna_summary sgRNA summary data generated by running MAGeCK RRA
RRApipeline Downstream analysis based on MAGeCK-RRA result
ScatterView Scatter plot
scatterview Scatter plot
Selector Select signatures from candidate list (according to the consistence in most samples).
sgRankView View sgRNA rank.
SquareView Scatter plot of 9-Square
squareview Scatter plot of 9-Square
TransGeneID Gene ID conversion between ENTREZID and SYMBOL
transGeneID Gene ID conversion between ENTREZID and SYMBOL
ViolinView Violin plot
violinview Violin plot
VolcanoView Volcano View
Zuber_Essential Core essential gene list