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 |