Man pages for baba-beda/morpheusR
Visual and interactive gene expression analysis
| adjustDataset | Adjust dataset |
| annotationDBMeta | Create meta file for AnnotationDB |
| calcPCA | Principal Component Analysis. |
| calculatedAnnotation | Create calculated annotation |
| checkGPLsFallback | Check possible annotations for GEO Dataset. |
| checkGSEType | Checks GSE to be supported |
| 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... |
| 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 |
| getCountsMetaPart | Create meta-data for single counts collection |
| 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 |
| isHSDS | check if url responding as HSDS server TRUE - hsds FALSE -... |
| limmaAnalysis | Differential Expression analysis. |
| loadCounts | Loads expression data from .h5 count files. Only samples with... |
| loadFromARCHS4 | Loads expression data from ARCHS4 count files. Only sapmles... |
| 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... |
| shinyGAMAnalysis | Constructs data frame with gene annotations and submits it... |
| subsetES | Subsets es, if rows or columns are not specified, all are... |
| updateARCHS4 | Update archs4 files. |
| updateARCHS4meta | Update ARCHS4 meta files |
| updateCountsMeta | Update meta-data for counts collections |
| updateDEE2meta | Update DEE2 meta files |
| validateCountsCollection | Check a counts collection |
| write.gct | Saves ExpressionSet to a GCT file (version 1.3). |
