# Visual and interactive gene expression analysis

## Documentation for package ‘phantasus’ version 1.0.2

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

## Help Pages

calcPCA | Principal Component Analysis.
checkGPLs | Check possible annotations for GEO Dataset.
checkPreloadedNames | Check names inside preloaded file
createES | Create ExpressionSet.
es | Example dataset
getES | Load ExpressionSet by GEO identifier
getGDS | Load ExpressionSet from GEO Datasets
getGSE | Load ExpressionSet from GEO Series
gseaPlot | Returns path to an svg file with enrichment plot
limmaAnalysis | Differential Expression analysis.
loadGEO | Load GEO Dataset.
loadPreloaded | Load GEO Dataset.
performKmeans | K-means clusterisation.
preloadedDirExists | Check existence of phantasusPreloadedDir
read.gct | Reads ExpressionSet from a GCT file.
reparseCachedESs | Reparse cached expression sets from GEO.
servePhantasus | Serve phantasus.
shinyGAMAnalysis | Constructs data frame with gene annotations and submits it into Shiny GAM web-server
subsetES | Subsets es, if rows or columns are not specified, all are retained
write.gct | Saves ExpressionSet to a GCT file (version 1.3).