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| RNAinteract-package | Analysis of Pairwise Interaction Screens. |
| bindscreens | bind RNAinteract objects along screens |
| computePI | compute pairwise interaction |
| computePValues | compute p-values |
| createCellHTSFromFiles | create cellHTS2 object from text files |
| createRNAinteract | create a RNAinteract object |
| createRNAinteractFromFiles | create an RNAinteract object from text files |
| doublePerturbationGrob | Double Perturbation Plot Grob |
| embedPCA | Computes a PCA for a pairwise interaction matrix. |
| endReport | start and end a RNAinteract report |
| estimateMainEffect | estimate main effect |
| getChannelNames | get names of screens and channels |
| getData | Primary access function for all screen data. |
| getIndDesignData | Extract replicates measurements from the screen. |
| getMain | get main effects |
| getMainNeg | get main effects |
| getReplicateData | Extract replicates measurements from the screen. |
| getScale | get scale information for a channel. |
| getScreenNames | get names of screens and channels |
| grid.doublePerturbation | Double Perturbation Plot Grob |
| grid.sgiHeatmap | A heatmap grob |
| normalizeMainEffectQuery | normalize query main effect |
| normalizeMainEffectTemplate | normalize template main effect |
| normalizePlateEffect | Normalization of plate effects |
| plotDoublePerturbation | Double Perturbation Plot |
| plotHeatmap | plots a heatmap for an interaction screen. |
| postDrawDetails.doublePerturbation | Double Perturbation Plot Grob |
| reportAnnotation | Specialized report functions |
| reportDoublePerturbation | Specialized report functions |
| reportGeneLists | Specialized report functions |
| reportHeatmap | Specialized report functions |
| reportMainEffects | Specialized report functions |
| reportNetworks | Specialized report functions |
| reportScreenData | Specialized report functions |
| reportStatistics | Specialized report functions |
| RNAinteract | Analysis of Pairwise Interaction Screens. |
| RNAinteract-class | Class "RNAinteract" |
| sgi | Dataset of class 'RNAinteract' |
| sgisubset | subset of an RNAinteract object. |
| sgisubsetQueryDesign | Subsetting query genes in a RNAinteract object. |
| show-method | Class "RNAinteract" |
| startReport | start and end a RNAinteract report |
| summarizeScreens | summarize screens |
| swaptree | Swaps a branch of a hclust object. |