ModuleRadarPlot
function to visualize expression levels of each module.PlotModuleTraitCorrelation
ModuleRadarPlot
New functionality and methods for module preservation analysis using the NetRep method from Ritchie et al 2016.
- ModuleTopologyHeatmap
function.
- ModuleTopologyBarplot
function.
- ModulePreservationNetrep
function.
- PlotModulePreservationLollipop
function.
ModulePreservation
FindDMEs
and FindAllDMEs
to perform differential testing with module expression scores.MetacellsByGroups
to specify dims
.HubGeneNetworkPlot
to allow selecting specific modules.GetHubGenes
now returns genes in order from highest to lowest kME in each module.EnrichrBarPlot
.ConstructNetwork
naming of temporary files updated.ConstructPseudobulk
. SetDatExpr
and SetMultiExpr
to use a pseudobulk expression matrix.RunEnrichr
to wait in between sending requests to the EnrichR server (default is 5 seconds).SetupForWGCNA
and SelectNetworkGenes
PlotDMEsLollipop
function to visualize differential module eigengenes.MetacellsByGroups
ResetModuleNames
and ResetModuleColors
to work when a grey module is not present.SetDatExpr
that would throw an error when group.by=NULL was selected.ReassignModules
that cause some modules assignments to be NA for some genes.PlotModuleTrajectory
function.ModuleConnectivity
and ReassignModules
.ReassignModules
function.ModuleConnectivity
to use corSparse
to compute the correlation, which greatly reduces runtime and memory usage.ModuleConnectivity
to automatically reassign features to different modules if kME is negative.ResetModuleNames
.MetaspotsByGroups
MetacellsByGroups
now keeps track of which cells were merged.SetupForWGCNA
if the user selects a very small number of genes.MetaspotsByGroups
uses sparse matrix format internally.MetaspotsByGroups
.MetaspotsByGroups
to aggregate neighboring ST spots prior to network analysis.TestSoftPowers
.MetacellsByGroups
to ensure that the selected slot is present in the selected assay.SetDatExpr
now backs up to the full dataset if the metacell dataset isn't found.ModuleConnectivity
that caused kMEs to be out of order.ModuleConnectivity
.exclude_grey
flag back to doing nothing in the ModuleEigengenes
function because it messed up some downstream tasks, will resolve in a future update.ProjectModules
now excludes modules with too many missing genes in the query dataset,
tunable by the overlap_proportion
parameter.ModuleEigengenes
does not compute MEs for the grey module. User can change behavior with the exclude_grey
flag.ProjectModules
.MetacellsByGroups
ModuleNetworkPlot
and RunModuleUMAP
now checks if ModuleConnectivity
has been computed in order to throw a more informative error.GetTOM
checks if the TOM file exists in order to throw a more informative error.MetacellsByGroups
if there are any groups that are excluded by min_cells
.MetacellsByGroups
, instead of the default "RNA".ModuleEigengenes
takes assay
as an argument, clears up some issues with RunHarmony
.ModuleEigengenes
doesn't require a "counts" slot to be present in the given assay, but now it throws an error if the normalized data slot is missing.ConstructNetwork
now checks if the TOM file already exists, and whether the user wants to overwrite the existing TOM.MetacellsByGroups
and ConstructMetacells
to exclude very small groups (min_cells
), to reach a target number of metacells (target_metacells
), and to exclude metacells with too much overlap (max_shared
).ModuleTraitCorrelation
can be run with a single trait.GetHubGenes
function to extract the top hub genes from the module assignment table.ConstructMetacells
stores run statistics as a table, and has a new option to exclude metacells that overlap with each other.ModuleEigengenes
checks to make sure the data has been scaled.PlotKMEs
so it would actually be included in the package.PlotKMEs
function to visualize the genes in a module ranked by kME.Add the following code to your website.
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