# Integrative analysis pipeline for pooled CRISPR functional genetic screens

## Documentation for package ‘MAGeCKFlute’ version 1.2.3

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

## Help Pages

arrangePathview | Kegg pathway view and arrange grobs on page
BatchRemove | Batch effect removal
CellCycle-method | Estimate cell cycle time for all samples compared to control sample and view.
CellCycleView | Estimate cell cycle time for all samples compared to control sample and view.
CorrView | Visualize the correlation between two object
countsummary | Count summary data generated by running MAGeCK count
CutoffCalling | Call cutoff
DensityDiffView | Density plot for beta score deviation between Control and Treatment
DensityView | Density plot for gene beta scores in Control and Treatment
enrich.GSE | GSEA
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
EnrichedGeneView | Visualize selected genes in enriched genesets
EnrichedGSEView | View enriched terms in GSEA
EnrichedView | View enriched terms
enrichGSE | GSEA
enrichgseview | View enriched terms in GSEA
enrichment | Enrichment analysis
enrichment_analysis | Enrichment analysis
enrichORT | Do enrichment analysis using over-representation test
EnrichSquare | Enrichment analysis for selected treatment related genes
enrichview | View enriched terms
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.
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