Man pages for phantasus
Visual and interactive gene expression analysis

adjustDatasetAdjust dataset
annotationDBMetaCreate meta file for AnnotationDB
calcPCAPrincipal Component Analysis.
calculatedAnnotationCreate calculated annotation
checkGPLsFallbackCheck possible annotations for GEO Dataset.
collapseDatasetCollapse dataset
colMeansByGroupsCalculate column averages in row groups
convertByAnnotationDBMap indexes using Annotation DB
createESCreate ExpressionSet.
esExample dataset
fgseaExampleExample pathway data.frame for fgsea tool
generatePreloadedSessionGenerate files for preloaded session from a session link.
getArchs4FilesReturns list of ARCHS4 hdf5 files with expression data
getESLoad ExpressionSet by GEO identifier
getGDSLoad ExpressionSet from GEO Datasets
getGSELoad ExpressionSet from GEO Series
gseaPlotReturns path to an svg file with enrichment plot
limmaAnalysisDifferential Expression analysis.
loadFromARCHS4Loads expression data from ARCHS4 count files. Only sapmles...
loadGEOLoad GEO Dataset.
loadPreloadedLoad GEO Dataset.
performKmeansK-means clusterisation.
queryAnnotationDBMetaGet meta list for annotationDB files
read.gctReads ExpressionSet from a GCT file.
reparseCachedESsReparse cached expression sets from GEO.
reproduceInRReproduce session in R code
servePhantasusServe phantasus.
shinyGAMAnalysisConstructs data frame with gene annotations and submits it...
subsetESSubsets es, if rows or columns are not specified, all are...
write.gctSaves ExpressionSet to a GCT file (version 1.3).
phantasus documentation built on Nov. 8, 2020, 6:39 p.m.