Man pages for shambam/cellexalvrR
Provides the backend calculations for CellexalVR
| addCellMeta2cellexalvr | Adds per cell metadata to a cellexalvrObj |
| addFACS2cellexalvr | Adds FACS index to a cellexalvrObj |
| addMDS2cellexalvr | Adds mds coordinates to a cellexalvrObj |
| branch.point.analysis | Performs a branch-point analysis identifying genes that have... |
| cellexalvr-class | Class defintion of cellexalvr |
| changeIdent | Sets new cell indentities from a given list |
| checkVRfiles | checkVRfiles: Checks the existance of all VR specific files... |
| defineGOIs | Allows the user to define (G)enes (O)f (I)nterest lists in... |
| Epigenetic | A simple table containing the data from... |
| export2cellexalvr | Creates the base files needed to run the VR environment |
| exportUserGroups4vr | Creates a summary file for the vr process |
| getDifferentials | Creates a heatmap from a selection of groups |
| get.genes.cor.to | Gets positively and negatively correlated genes to a chosen... |
| groupingInfo | returns the information stored for the last grouping read |
| human.tfs | A list of human transcription factors. |
| loadObject | Loads the cellexalvr object, if the fname is a file |
| lockedSave | Saving the RData in the VR tool might create a problem. Hence... |
| make.cellexalvr.heatmap | Creates a heatmap from a selection of groups |
| make.cellexalvr.heatmap.list | Creates a list of genes from which a heatmap is made in Unity |
| make.cellexalvr.network | Creates a network from selected groups for selected genes |
| MakeCellexaVRObj | Creates a cellexalvr objext with the data given |
| make.cell.meta.from.df | Creates a meta cell matrix from a supplied dataframe from... |
| mouse.tfs | A list of mouse transcription factors. |
| onlyGOIs | Allows the user to select only (G)enes (O)f (I)nterest lists... |
| plotAllMDS | Plots the MDS reduced data for a quick look |
| print-methods | description of function print |
| reduceTo-methods | description of function reduceTo |
| renew-methods | description of function renew |
| reorder.genes-methods | description of function remove.genes |
| reorder.samples-methods | description of function remove.genes |
| run.ddrtree | Runs DDRtree for a Seurat class |
| set.specie | Loads TF annotation into cellexalvr object |
| seurat2cellexalvr | Converts a seurat class to one of cellexalvr. If the... |
| useInbuiltGOIlists-methods | description of function useInbuiltGOIlists |
| userGrouping | Reads a VR cell selection file and creates a user.grouping... |
