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| 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 for gene beta scores in Control and Treatment |
| enrich.GSE | Gene set enrichment analysis |
| 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 |
| 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 |
| enrichGSE | Gene set enrichment analysis |
| enrichment | Enrichment analysis |
| enrichORT | Do enrichment analysis using over-representation test |
| EnrichSquare | Enrichment analysis for selected treatment related genes |
| FluteMLE | Downstream analysis based on MAGeCK-MLE result |
| 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 databases. |
| 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 |
| loess.normalize | normalize.loess |
| MapRatesView | View mapping ratio |
| MAView | MAplot of gene beta scores |
| noEnrichPlot | Blank figure |
| normalize.loess | normalize.loess |
| NormalizeBeta | Normalize gene beta scores |
| normalizebeta | Normalize gene beta scores |
| OmitCommonEssential | Omit common essential genes based on depmap data |
| 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 |
| ResembleDepmap | Compute the similarity between customized CRISPR screen with Depmap screens |
| retrieve_gs | Update genesets from source database |
| RRApipeline | Downstream analysis based on MAGeCK-RRA result |
| 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 |
| writeGMT | ReadGMT |