Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

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Documentation for package ‘MAGeCKFlute’ version 2.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

arrangePathview	Kegg pathway view and arrange grobs on page
BarView	Bar plot
BatchRemove	Batch effect removal
ConsistencyView	Visualize the estimate cell cycle compared to control.
CutoffCalling	Quantile of normal distribution.
DensityDiffView	Density plot
DensityView	Density plot
enrich.GSE	Gene set enrichment analysis
enrich.HGT	Do enrichment analysis using hypergeometric test
enrich.ORT	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	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
getCols	Map values to colors
getGeneAnn	Retrieve gene annotations from the NCBI, HNSC, and Uniprot databases.
getOrg	Get the kegg code of specific mammalia organism.
getOrtAnn	Retreive reference orthologs annotation.
gsGetter	Extract pathway annotation from GMT file.
hclustView	Cluster and view cluster tree
HeatmapView	Draw heatmap
IdentBarView	Identical bar plot
IncorporateDepmap	Incorporate Depmap screen into analysis
LoadDepmap	Load processed Depmap data
loadDepmap	Load processed Depmap data
loess.normalize	normalize.loess
MapRatesView	View mapping ratio
MAView	MAplot of gene beta scores
noEnrichPlot	Blank figure
normalize.loess	normalize.loess
NormalizeBeta	Normalize gene beta scores
normalizebeta	Normalize gene beta scores
OmitCommonEssential	Omit common essential genes based on depmap data
RankView	Rank plot
rankview	Rank plot
ReadBeta	Read gene beta scores from MAGeCK-MLE results
readbeta	Read gene beta scores from MAGeCK-MLE results
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
ResembleDepmap	Compute the similarity between customized CRISPR screen with Depmap screens
retrieve_gs	Update genesets from source database
RRApipeline	Downstream analysis based on MAGeCK-RRA result
ScatterView	Scatter plot
Selector	Select signatures from candidate list (according to the consistence in most samples).
sgRankView	View sgRNA rank.
SquareView	Scatter plot showing dots in 9 quadrants
squareview	Scatter plot showing dots in 9 quadrants
TransGeneID	Gene ID conversion
ViolinView	Violin plot
violinview	Violin plot
VolcanoView	Volcano View
writeGMT	Write GMT file