Man pages for KrishnaswamyLab/phemd
Phenotypic EMD for comparison of single-cell samples
| 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... |
| assignCellClusterNearestNode | Assign cells to a reference cell subtype |
| batchIDs | Accessor function for batch ID for each sample |
| bindSeuratObj | Attach 'Seurat' object to 'Phemd' object |
| celltypeFreqs | Accessor function for cell subtype distribution for each... |
| clusterIndividualSamples | Computes cell subtype abundances for each sample |
| compareSamples | Computes EMD distance matrix representing pairwise... |
| 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... |
| GDM | Accessor function for EMD ground distance matrix |
| 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... |
| getSampleSizes | Retrieve single-cell sample sizes |
| groupSamples | Performs community detection on sample-sample distance matrix... |
| heatmap_genes | Genes to be used when plotting heatmap for melanoma... |
| identifyCentroids | Identify cluster centroids (cell names) |
| monocleInfo | Accessor function for stored Monocle object |
| orderCellsMonocle | Compute Monocle2 cell state and pseudotime assignments |
| phateInfo | Accessor function for stored phate object |
| Phemd | Phemd class |
| 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... |
| plotHeatmaps | Plot heatmap of cell subtypes |
| plotSummaryHistograms | Plots cell subtype frequency histograms summarizing each... |
| pooledCells | Accessor function for aggregated cells used for cell subtype... |
| printClusterAssignments | Writes samples to file based on community detection group... |
| rawExpn | Accessor function for stored multi-sample raw expression data |
| removeTinySamples | Remove samples with too few cells |
| retrieveRefClusters | Retrieve reference cell clusters |
| selected_genes | Genes to be used when performing clustering and trajectory... |
| selectFeatures | Perform feature selection on aggregated data |
| selectMarkers | Accessor function for gene/protein markers measured in... |
| seuratInfo | Accessor function for stored Seurat object within Phemd... |
| sNames | Accessor function for identifiers of all single-cell samples... |
| snames_data | Sample names for melanoma single-cell RNA-seq expression data |
| subsampledBool | Accessor function for whether or not cells were subsampled... |
| subsampledIdx | Accessor function for aggregated cells used for cell subtype... |
