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| 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 |