adjustDataset           Adjust dataset
annotationDBMeta        Create meta file for AnnotationDB
calcPCA                 Principal Component Analysis.
calculatedAnnotation    Create calculated annotation
checkGPLsFallback       Check possible annotations for GEO Dataset.
colMeansByGroups        Calculate column averages in row groups
collapseDataset         Collapse dataset
convertByAnnotationDB   Map indexes using Annotation DB
createES                Create ExpressionSet.
es                      Example dataset
fgseaExample            Example pathway data.frame for fgsea tool
generatePreloadedSession
                        Generate files for preloaded session from a
                        session link.
getArchs4Files          Returns list of ARCHS4 hdf5 files with
                        expression data
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.
loadCounts              Loads expression data from .h5 count files.
                        Only sapmles with counted expression are kept.
                        If es already containts expression data it is
                        returned as is.
loadFromARCHS4          Loads expression data from ARCHS4 count files.
                        Only sapmles with counted expression are kept.
                        If es already containts expression data it is
                        returned as is.
loadGEO                 Load GEO Dataset.
loadPreloaded           Load GEO Dataset.
performKmeans           K-means clusterisation.
queryAnnotationDBMeta   Get meta list for annotationDB files
read.gct                Reads ExpressionSet from a GCT file.
reparseCachedESs        Reparse cached expression sets from GEO.
reproduceInR            Reproduce session in R code
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).
