Man pages for symphony
Efficient and Precise Single-Cell Reference Atlas Mapping
| buildReference | Function for building a Symphony reference starting from... |
| buildReferenceFromHarmonyObj | Function for building a Symphony reference from a Harmony... |
| calcknncorr | Calculates the k-NN correlation, which measures how well the... |
| calcknncorrWithinQuery | Calculates the k-NN correlation within the query cells only,... |
| calcPerCellMappingMetric | Per-cell Confidence Score: Calculates the weighted... |
| calcPerClusterMappingMetric | Per-cluster Confidence Score: Calculates the Mahalanobis... |
| evaluate | Function for evaluating F1 by cell type, adapted from... |
| findVariableGenes | Function to find variable genes using mean variance... |
| knnPredict | Predict annotations of query cells from the reference using... |
| mapQuery | Function for mapping query cells to a Symphony reference |
| pbmcs_exprs_small | Log(CP10k+1) normalized counts matrix (genes by cells) for... |
| pbmcs_meta_small | Metadata for 10x PBMCs dataset for vignette. |
| plotReference | Function to plot reference, colored by cell type |
| rowSDs | Calculate standard deviations by row |
| runPCAQueryAlone | Runs a standard PCA pipeline on query (1 batch). Assumes... |
| scaleDataWithStats | Scale data with given mean and standard deviations |
| symphony | symphony |
| vargenes_vst | Function to find variable genes using variance stabilizing... |
