Man pages for MAGeCKFlute
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

arrangePathviewKegg pathway view and arrange grobs on page
BarViewBar plot
BatchRemoveBatch effect removal
ConsistencyViewVisualize the estimate cell cycle compared to control.
CutoffCallingQuantile of normal distribution.
DensityDiffViewDensity plot
DensityViewDensity plot for gene beta scores in Control and Treatment
EnrichABEnrichment analysis for Positive and Negative selection genes
EnrichAnalyzerEnrichment analysis
EnrichedFilterSimplify the enrichment results based on Jaccard index
EnrichedGeneViewVisualize enriched pathways and genes in those pathways
EnrichedViewView enriched terms
enrich.GSEGene set enrichment analysis
enrich.HGTDo enrichment analysis using hypergeometric test
enrich.ORTDo enrichment analysis using over-representation test
EnrichSquareEnrichment analysis for selected treatment related genes
FluteMLEDownstream analysis based on MAGeCK-MLE result
FluteRRADownstream analysis based on MAGeCK-RRA result
getColsMap values to colors
getGeneAnnRetrieve gene annotations from the NCBI, HNSC, and Uniprot...
getOrgGet the kegg code of specific mammalia organism.
getOrtAnnRetreive reference orthologs annotation.
gsGetterExtract pathway annotation from GMT file.
hclustViewCluster and view cluster tree
HeatmapViewDraw heatmap
IdentBarViewIdentical bar plot
IncorporateDepmapIncorporate Depmap screen into analysis
MapRatesViewView mapping ratio
MAViewMAplot of gene beta scores
noEnrichPlotBlank figure
NormalizeBetaNormalize gene beta scores
OmitCommonEssentialOmit common essential genes based on depmap data
RankViewView the rank of gene points
ReadBetaRead gene beta scores
ReadRRARead gene summary file in MAGeCK-RRA results
ReadsgRRARead sgRNA summary in MAGeCK-RRA results
reexportsObjects exported from other packages
ResembleDepmapCompute the similarity between customized CRISPR screen with...
retrieve_gsUpdate genesets from source database
ScatterViewScatter plot
SelectorSelect signatures from candidate list (according to the...
sgRankViewView sgRNA rank.
SquareViewScatter plot of 9-Square
TransGeneIDGene ID conversion between ENTREZID and SYMBOL
ViolinViewViolin plot
VolcanoViewVolcano View
MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.