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
exprspca                Perform PCA and prepare results for
                        'omicsViewer'
extendMetaData          Add extra columns to the phenoData/colData or
                        featureData/rowData in
                        ExpressionSet/SummarizedExperiment
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
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
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
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
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
