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 |
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 |
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 |
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 |