# Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

## Documentation for package ‘MAGeCKFlute’ version 2.0.0

- 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