aggregateSamples | Aggregate expression data from all samples |
all_expn_data | Single-cell RNA-seq expression data for melanoma samples |
all_genes | All genes included in (subsampled) melanoma single-cell RNA-seq expression data |
assignCellClusterNearestNode | Assign cells to a reference cell subtype |
batchIDs | Accessor function for batch ID for each sample |
batchIDs<- | Setter function for protein / gene markers |
batchIDs<--method | Setter function for protein / gene markers |
bindSeuratObj | Attach 'Seurat' object to 'Phemd' object |
celltypeFreqs | Accessor function for cell subtype distribution for each sample |
celltypeFreqs<- | Setter function for protein / gene markers |
celltypeFreqs<--method | Setter function for protein / gene markers |
clusterIndividualSamples | Computes cell subtype abundances for each sample |
compareSamples | Computes EMD distance matrix representing pairwise dissimilarity between samples |
createDataObj | Create 'Phemd' object |
drawColnames45 | Rotates heatmap marker labels 45 degrees |
embedCells | Generate cell-state embedding |
gaussianffLocal | Models expression data using generalized linear model with Gaussian error |
GDM | Accessor function for EMD ground distance matrix |
GDM<- | Setter function for protein / gene markers |
GDM<--method | Setter function for protein / gene markers |
generateGDM | Computes ground distance matrix based on cell embedding |
getArithmeticCentroids | Get arithmetic centroids (coordinates) |
getCellYield | Gets cell yield of each sample as a table |
getSampleCelltypeFreqs | Returns cell subtype distribution for each sample as a table |
getSampleHistsByCluster | Gets cell subtype frequency histograms for each sample by cluster ID |
getSampleSizes | Retrieve single-cell sample sizes |
groupSamples | Performs community detection on sample-sample distance matrix to identify groups of similar samples |
heatmap_genes | Genes to be used when plotting heatmap for melanoma single-cell RNA-seq expression data |
identifyCentroids | Identify cluster centroids (cell names) |
monocleInfo | Accessor function for stored Monocle object |
monocleInfo<- | Setter function for protein / gene markers |
monocleInfo<--method | Setter function for protein / gene markers |
orderCellsMonocle | Compute Monocle2 cell state and pseudotime assignments |
phateInfo | Accessor function for stored phate object |
phateInfo<- | Setter function for protein / gene markers |
phateInfo<--method | Setter function for protein / gene markers |
Phemd | Phemd class |
Phemd-class | Phemd class |
Phemd-method | Setter function for protein / gene markers |
Phemd-methods | Setter function for protein / gene markers |
plotCellYield | Plot cell yield of each sample as bar plot |
plotEmbeddings | Plots Monocle2 cell embedding plots |
plotGroupedSamplesDmap | Plot diffusion map embedding of samples based on distance matrix |
plotHeatmaps | Plot heatmap of cell subtypes |
plotSummaryHistograms | Plots cell subtype frequency histograms summarizing each group of samples |
pooledCells | Accessor function for aggregated cells used for cell subtype definition |
pooledCells<- | Setter function for protein / gene markers |
pooledCells<--method | Setter function for protein / gene markers |
printClusterAssignments | Writes samples to file based on community detection group assignments |
rawExpn | Accessor function for stored multi-sample raw expression data |
rawExpn<- | Setter function for protein / gene markers |
rawExpn<--method | Setter function for protein / gene markers |
removeTinySamples | Remove samples with too few cells |
retrieveRefClusters | Retrieve reference cell clusters |
selected_genes | Genes to be used when performing clustering and trajectory analyses on melanoma single-cell RNA-seq expression data |
selectFeatures | Perform feature selection on aggregated data |
selectMarkers | Accessor function for gene/protein markers measured in experiment |
selectMarkers<- | Setter function for protein / gene markers |
selectMarkers<--method | Setter function for protein / gene markers |
seuratInfo | Accessor function for stored Seurat object within Phemd object |
seuratInfo<- | Setter function for protein / gene markers |
seuratInfo<--method | Setter function for protein / gene markers |
sNames | Accessor function for identifiers of all single-cell samples in experiment |
snames_data | Sample names for melanoma single-cell RNA-seq expression data |
subsampledBool | Accessor function for whether or not cells were subsampled when aggregated for cell subtype analysis |
subsampledBool<- | Setter function for protein / gene markers |
subsampledBool<--method | Setter function for protein / gene markers |
subsampledIdx | Accessor function for aggregated cells used for cell subtype definition |
subsampledIdx<- | Setter function for protein / gene markers |
subsampledIdx<--method | Setter function for protein / gene markers |