|
ApplyCountThreshold()
|
Remove rare and ubiquitous genes |
|
AvgFeatureExpression()
|
Find average cluster feature expression |
|
ClusterAvg()
|
Create a heatmap with signaling markers over clusters |
|
ClusterCells()
|
Cluster the Cells |
|
ClusterSig()
|
Average cluster to cluster signaling. |
|
ClusterSig_single()
|
Average cluster to cluster signaling. |
|
ColorHue()
|
Get a vector of n equally spaced rgb colors |
|
CountClusters()
|
Use clustering consensus to infer cluster number |
|
FeatureScatterPlot()
|
Produce a scatter plot of the cells |
|
FindRootCell()
|
Find the root cell |
|
FindRootCluster()
|
Find the root cluster |
|
GetCellMetric()
|
Get metric of pseudotime |
|
GetComponents()
|
Get graph components |
|
GetConsensus()
|
Produce a consensus matrix |
|
GetCorrelation()
|
Get rank correlation |
|
GetDGFromTable()
|
Get a weighted, directed graph from a table of edges and weights |
|
GetDominatorTree()
|
Get a directed graph from a predecessor vector |
|
GetEnsemble()
|
Produce consensus matrix |
|
GetMarkerTable()
|
Get the marker genes for each cluster |
|
GetPredecessors()
|
Get the predecessor vector for a dominator tree encoded as an undirected tree and root |
|
GetSignalingPartners()
|
Compute Cell-cell interaction probability |
|
ImportPathway()
|
Process siganling pathway data |
|
JoinGraphComponents()
|
Join Graph Components |
|
LoadData()
|
Load sequencing data and annotations |
|
LogNormalize()
|
Scale and center a data matrix |
|
MembershipList()
|
Get a list of membership vectors |
|
PlotClusterExpression()
|
Heatmap of specific genes |
|
PlotLineage()
|
Plot the pseudotime ordering of clusters |
|
PlotMatlabDtree()
|
Produce a plot of matlab DTree data and return the object |
|
PlotTopN()
|
Heatmap of the top n markers |
|
PlotTopN_Grid()
|
Factor Grid heatmap of the top n markers |
|
ProcessMatlabDTree()
|
Convert a matlab edge table and predecessor list into a directed weighted edge table |
|
RepresentationMap()
|
Generate multiple representations |
|
ScaleCenterData()
|
Scale and center a data matrix |
|
SelectData()
|
Set of the most variable genes |
|
SigPlot()
|
Heatmap plot of cell signaling |
|
SigPlot_Cluster()
|
Heatmap plot of cluster signaling |
|
SimilarityM()
|
Compute the similarity matrix |
|
SimpleCap()
|
Capitalize the first letter of a string |
|
ViolinPlotExpression()
|
Violin plot of gene expression |
|
computeM()
|
Perform ADMM |
|
getAlpha()
|
compute lig and rec |
|
getBetaj()
|
compute uptargets |
|
getGammaj()
|
compute downtargets |
|
updateFlatBoth()
|
compute the unnormalized probability |
|
updateFlatDown()
|
compute the unnormalized probability |
|
updateFlatNone()
|
compute the unnormalized probability |
|
updateFlatUp()
|
compute the unnormalized probability |