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| RNAither-package | Statistical analysis of high-throughput RNAi screens |
| BScore | BScore normalization |
| channelPlot | Plot signal channels against each other |
| closestToZero | Return the replicate value closest to zero |
| compareHits | Searching for common hits between different scoring methods |
| compareReplicaPlates | Compare replica plates |
| compareReplicates | Compare replicate values |
| compareReplicateSD | Plot the standard deviation of replicates |
| compareReplicateSDPerScreen | Plot the standard deviation of replicates for each experiment |
| controlDensity | Plotting the control density |
| controlDensityPerPlate | Plotting the control density per plate |
| controlDensityPerScreen | Plotting the control density per experiment |
| controlNorm | Normalization on controls |
| createSubset | Creating a subset of a dataset according to a certain column value |
| dataset | a typical example RNAi dataset |
| datasetDrosophila | Genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al. |
| discardLabtek | Remove a complete plate from the analysis |
| discardWells | Remove wells from the analysis |
| divideChannels | Divide channel values |
| divNorm | Mean, median, ... , normalization |
| DRQualControl | Computing the dynamic range |
| eraseDataSetColumn | Remove columns from dataset |
| findReplicates | Find all replicates of a certain siRNA/gene in a dataset |
| furthestFromZero | Return the replicate value furthest from zero |
| generateDatasetFile | Generate Dataset File |
| generateReplicateMat | Generate a matrix of replicates |
| generateRepMatNoFilter | Generate a matrix of replicates (II) |
| gseaAnalysis | Perform a GSEA analysis of a list of genes |
| header | a typical header of an example RNAi dataset |
| headerDrosophila | the header of the genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al. |
| hitselectionPval | Selecting hits according to p-values |
| hitselectionZscore | Selecting hits according to ZScores |
| hitselectionZscorePval | Selecting hits according to ZScores and p-values |
| incorporatepValVec | Incorporate a vector of p-values into a dataset |
| indexSubset | Saving the indexes of a subset in the main dataset |
| joinDatasetFiles | Join dataset files |
| joinDatasets | Join datasets |
| LiWongRank | Li Wong rank / invariant probeset normalization |
| lowessNorm | Lowess normalization |
| mainAnalysis | Wrapper function for full automated analysis |
| makeBoxplot4PlateType | Generate a boxplot of the data per plate |
| makeBoxplotControls | Generate a boxplot of the data vs. the controls |
| makeBoxplotControlsPerPlate | Generate a boxplot of the data vs. the controls for each plate |
| makeBoxplotControlsPerScreen | Generate a boxplot of the data vs. the controls for each experiment |
| makeBoxplotPerPlate | Generate a boxplot of the data per plate |
| makeBoxplotPerScreen | Generate a boxplot of the data per experiment |
| MannWhitney | Perform a Mann-Whitney test |
| multTestAdjust | Adjust p-values for multiple testing |
| numCellQualControl | Quality control of the number of cells |
| orderGeneIDs | Order a dataset |
| percCellQualControl | Quality control of the percentage of cells |
| plotBar | Plot signal intensities per well |
| plotControlHisto | Plot a histogram of the data values and controls |
| plotControlHistoPerplate | Plot a histogram of the data values and controls per plate |
| plotControlHistoPerscreen | Plot a histogram of the data values and controls per experiment |
| plotHisto | Plot a histogram of the data values |
| plotHistoPerplate | Plot a histogram of the data values per plate |
| plotHistoPerscreen | Plot a histogram of the data values per experiment |
| plotQQ | Make a QQ plot |
| plotQQperplate | Make a QQ plot per plate |
| plotQQperscreen | Make a QQ plot per experiment |
| pValVec1 | A vector of p-values after a median normalization and a t-test |
| pValVec2 | A vector of p-values after a Mann-Whitney test |
| quantileNormalization | Quantile normalization |
| RankProduct | Perform a Rank Product test |
| replicatesCV | Compute the correlation of variation (CV) |
| replicatesSpearmancor | Compute the correlation coefficient betwenn replicates or experiments |
| rms | Compute the replicate root mean square |
| RNAither | Statistical analysis of high-throughput RNAi screens |
| rnaither | Wrapper function for full automated analysis |
| saveDataset | Save the normalized dataset into a dataset text file |
| saveOldIntensityColumns | Save old intensity value columns |
| savepValVec | Save p-values to file |
| scoredDataset1 | A dataset containing an additional column showing the p-values, after a median normalization and a t-test |
| scoredDataset2 | A dataset containing an additional column showing the p-values after a Mann-Whitney test |
| SNRQualControl | Computing the SNR |
| spatialDistrib | Generate spatial plots of intensity values |
| spatialDistribHits | Plotting the spatial distribution of the hits |
| subtractBackground | Background substraction |
| sumChannels | Summarize channels |
| summarizeReps | Generate a new dataset with summarized replicates |
| summarizeRepsNoFiltering | Generate a new dataset with summarized replicates |
| trim | Compute the replicate mean with trimmed values |
| Ttest | Perform a Student's t-test |
| varAdjust | Variance adjustment |
| vennDiag | Plotting a Venn Diagram to compare hits |
| volcanoPlot | Making a volcano plot |
| ZPRIMEQualControl | Computing the Z' factor |
| ZScore | ZScore normalization |
| ZScorePerScreen | ZScore normalization per experiment |
| ZScorePlot | Plot normalized intensity values per well |
| ZScorePlotTwo | Plot signal intensities per well (II) |