| .e2EC50 | convert e (inflection point) to EC50 |
| .modelFormula | model fitted by drc |
| app_module | Application level 0 module |
| app_ui | Application level 0 UI |
| asEsetWithAttr | Convert SummarizedExperiment to ExpressionSet retaining all attributes |
| correlationAnalysis | Correlating a expression matrix with phenotypical variables |
| csc2list | convert a column compressed sparse matrix to a list |
| downloadUPRefProteome | get uniprot reference proteome IDs |
| draw_roc_pr | Drawing ROC and PR curve |
| drmMat | Fitting dose-response models for omics data matrix |
| exprspca | Perform PCA and prepare results for 'omicsViewer' |
| extendMetaData | Add extra columns to the phenoData/colData or featureData/rowData in ExpressionSet/SummarizedExperiment |
| extendMetaData-method | Add extra columns to the phenoData/colData or featureData/rowData in ExpressionSet/SummarizedExperiment |
| extractParamDC | Extracting parameters from drc models |
| extractParamDCList | Extracting parameter from a list of drc object |
| fgsea1 | Wrapper of fgseaMultilevel function to take binary gene set matrix as input |
| fillNA | Filling NAs in a matrix using constants calculated from user the defined function |
| filterRow | Filter out rows of expression matrix |
| getAutoRIF | Get genes associated with search terms and AutoRIF annotations |
| getMQParams | Parse mqpar.xml file |
| getUPRefProteomeID | get uniprot reference proteome IDs |
| gsAnnotIdList | Annotation of gene/protein function using multiple IDs. |
| hasAttr | Check whether an object has an attribute |
| hclust2str | Convert hclust object to/from single character |
| jaccardList | Calculate Jaccard distance from a list |
| list2csc | convert a list to column compressed sparse matrix |
| multi.t.test | Function to perform multiple t-tests on an expression matrix |
| nColors | Generating k distinct colors |
| normalize.nQuantiles | Normalization using n quantiles |
| normalize.totsum | Normalize total sum |
| normalizeColWise | Column-wise normalization of expression matrix |
| normalizeData | Normalized expression matrix |
| omicsViewer | Start omicsViewer |
| parseDatTerm | Extract function annotation from uniprot .dat file |
| plotDC | Draw dose-response curves |
| plotDCMat | Draw dose response curve given parameters in the omicsViewer object |
| plotly_boxplot_module | Shiny module for boxplot using plotly - Module |
| plotly_boxplot_ui | Shiny module for boxplot using plotly - UI |
| plotly_scatter_module | Shiny module for scatter plot using plotly - Module |
| plotly_scatter_ui | Shiny module for scatter plot using plotly - UI |
| plot_roc_pr_module | Shiny module for boxplot using plotly - Module |
| prepOmicsViewer | Prepare object to be viewed by omicsViewer |
| read.proteinGroups | Reading proteinGroup table of MaxQuant output |
| read.proteinGroups.lf | Read protein groups output of maxquant output and split it to columns |
| readESVObj | Read the object of SummarizedExperiment or ExpressetSet to be visualized using omicsViewer |
| read_gmt | Reading gene set .gmt file |
| removeVarQC | Removing variance of reference samples |
| rowshift | Row-wise normalization of expression matrix with or without reference sample |
| saveOmicsViewerDb | Save the xcmsViewer result object as sqlite database |
| saveOmicsViewerDb-method | Save the xcmsViewer result object as sqlite database |
| str2hclust | Convert hclust object to/from single character |
| triselector_module | The three-step selector - the module function |
| triselector_ui | The three-step selector - the ui function |
| trisetter | Create a nx3 matrix that can be use for triselector given a meta and expression table |
| validMQFolder | MQ folder validator Validate whether a folder is a MQ output folder |
| varSelector | variable selector |