Man pages for shambam/cellexalvrR
Provides the backend calculations for CellexalVR

addCellMeta2cellexalvrAdds per cell metadata to a cellexalvrObj
addFACS2cellexalvrAdds FACS index to a cellexalvrObj
addMDS2cellexalvrAdds mds coordinates to a cellexalvrObj
branch.point.analysisPerforms a branch-point analysis identifying genes that have...
cellexalvr-classClass defintion of cellexalvr
changeIdentSets new cell indentities from a given list
checkVRfilescheckVRfiles: Checks the existance of all VR specific files...
defineGOIsAllows the user to define (G)enes (O)f (I)nterest lists in...
EpigeneticA simple table containing the data from...
export2cellexalvrCreates the base files needed to run the VR environment
exportUserGroups4vrCreates a summary file for the vr process
getDifferentialsCreates a heatmap from a selection of groups
get.genes.cor.toGets positively and negatively correlated genes to a chosen...
groupingInforeturns the information stored for the last grouping read
human.tfsA list of human transcription factors.
loadObjectLoads the cellexalvr object, if the fname is a file
lockedSaveSaving the RData in the VR tool might create a problem. Hence...
make.cellexalvr.heatmapCreates a heatmap from a selection of groups
make.cellexalvr.heatmap.listCreates a list of genes from which a heatmap is made in Unity
make.cellexalvr.networkCreates a network from selected groups for selected genes
MakeCellexaVRObjCreates a cellexalvr objext with the data given
make.cell.meta.from.dfCreates a meta cell matrix from a supplied dataframe from...
mouse.tfsA list of mouse transcription factors.
onlyGOIsAllows the user to select only (G)enes (O)f (I)nterest lists...
plotAllMDSPlots the MDS reduced data for a quick look
print-methodsdescription of function print
reduceTo-methodsdescription of function reduceTo
renew-methodsdescription of function renew
reorder.genes-methodsdescription of function remove.genes
reorder.samples-methodsdescription of function remove.genes
run.ddrtreeRuns DDRtree for a Seurat class
set.specieLoads TF annotation into cellexalvr object
seurat2cellexalvrConverts a seurat class to one of cellexalvr. If the...
useInbuiltGOIlists-methodsdescription of function useInbuiltGOIlists
userGroupingReads a VR cell selection file and creates a user.grouping...
shambam/cellexalvrR documentation built on May 6, 2018, 10:47 p.m.