Efficient and Precise Single-Cell Reference Atlas Mapping
Function for building a Symphony reference starting from expression ma...
Function for building a Symphony reference from a Harmony object. Usef...
Calculates the k-NN correlation, which measures how well the sorted or...
Calculates the k-NN correlation within the query cells only, which mea...
Per-cell Confidence Score: Calculates the weighted Mahalanobis distanc...
Per-cluster Confidence Score: Calculates the Mahalanobis distance from...
Function for evaluating F1 by cell type, adapted from automated cell t...
Function to find variable genes using mean variance relationship metho...
Predict annotations of query cells from the reference using k-NN metho...
Function for mapping query cells to a Symphony reference
Function to plot reference, colored by cell type
Calculate standard deviations by row
Runs a standard PCA pipeline on query (1 batch). Assumes query_exp is ...
Scale data with given mean and standard deviations
symphony
Function to find variable genes using variance stabilizing transform (...
Implements the Symphony single-cell reference building and query mapping algorithms and additional functions described in Kang et al <https://www.nature.com/articles/s41467-021-25957-x>.