adjustDataset | Adjust dataset |
annotationDBMeta | Create meta file for AnnotationDB |
calcPCA | Principal Component Analysis. |
calculatedAnnotation | Create calculated annotation |
checkGPLsFallback | Check possible annotations for GEO Dataset. |
collapseDataset | Collapse dataset |
colMeansByGroups | Calculate column averages in row groups |
convertByAnnotationDB | Map indexes using Annotation DB |
createDockerConf | Creates default docker conf file Function creates default docker user configuration file based on provided 'setup_file' or on default parameters if 'setup_file' doesn't exist. If 'user_conf_file' exists function does nothing. |
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 |
getPhantasusConf | Read Phantasus Config |
gseaPlot | Returns path to an svg file with enrichment plot |
limmaAnalysis | Differential Expression analysis. |
loadCounts | Loads expression data from .h5 count files. Only samples 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. |
setupPhantasus | Setup phantasus. Read user config file ( or create default one) and fill 'cache_root' using sources in 'file'. |
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 |
updateARCHS4 | Update archs4 files. |
updateARCHS4meta | Update ARCHS4 meta files |
updateCountsMeta | Update meta-data for counts collections |
updateDEE2meta | Update DEE2 meta files |
write.gct | Saves ExpressionSet to a GCT file (version 1.3). |