Charlotte A. Darby

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

scHLAcount computes allele-specific HLA expression from single-cell RNA-seq data, revealing cell-type and tumor-normal differences in allelic patterns.

Vargas provides a heuristic-free read aligner that computes optimal alignments for linear and graph genomes, improving alignment accuracy by optimizing parameters in existing aligners.

Samovar calls mosaic SNVs in single samples using linked-read data with accuracy comparable to trio or tumor/normal pair analyses.

LRSim generates linked reads to evaluate genome partitioning strategies and provides recommendations for sequencing parameters.