Man pages for WubingZhang/MAGeCKFlute
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
| 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 |
| 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 |
| enrich.GSE | Gene set enrichment analysis |
| enrich.HGT | Do enrichment analysis using hypergeometric test |
| enrich.ORT | Enrichment analysis using over-representation test |
| EnrichSquare | Enrichment analysis for selected treatment related genes |
| 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... |
| 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 |
| MapRatesView | View mapping ratio |
| MAView | MAplot of gene beta scores |
| noEnrichPlot | Blank figure |
| NormalizeBeta | Normalize gene beta scores |
| normalize.loess | normalize.loess |
| OmitCommonEssential | Omit common essential genes based on depmap data |
| RankView | Rank plot |
| ReadBeta | Read gene beta scores from MAGeCK-MLE results |
| ReadGMT | ReadGMT |
| ReadRRA | Read gene summary file in MAGeCK-RRA results |
| ReadsgRRA | Read sgRNA summary in MAGeCK-RRA results |
| reexports | Objects exported from other packages |
| ResembleDepmap | Compute the similarity between customized CRISPR screen with... |
| retrieve_gs | Update genesets from source database |
| ScatterView | Scatter plot |
| Selector | Select signatures from candidate list (according to the... |
| sgRankView | View sgRNA rank. |
| SquareView | Scatter plot showing dots in 9 quadrants |
| TransGeneID | Gene ID conversion |
| ViolinView | Violin plot |
| VolcanoView | Volcano View |
| writeGMT | Write GMT file |
