Integrative analysis pipeline for pooled CRISPR functional genetic screens


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Documentation for package ‘MAGeCKFlute’ version 1.0.1

Help Pages

arrangePathview Kegg pathway view and arrange grobs on page
BatchRemove Batch effect removal
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
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.DAVID Do enrichment analysis using DAVID
enrich.GOstats Do enrichment analysis using GOstats
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
enrichDAVID Do enrichment analysis using DAVID
EnrichedGSEView View enriched terms in GSEA
EnrichedView View enriched terms
enrichGOstats Do enrichment analysis using GOstats
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 Calculate the similarity between samples and plot heatmap
heatmapview Calculate the similarity between samples and plot 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_Data Gene summary table in MAGeCK MLE results
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
ReadRRA Read MAGeCK-RRA data
readrra Read MAGeCK-RRA data
RRApipeline Downstream analysis based on MAGeCK-RRA result
RRA_Data Gene summary data generated by running MAGeCK RRA
ScatterView Scatter plot
scatterview Scatter plot
Selector Select signatures from candidate list (according to the consistence in most samples).
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
Zuber_Essential Core essential gene list