Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer

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Documentation for package ‘omicsViewer’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
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
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