RobustClone

RobustClone infers subclonal genotypes and evolutionary trees from single-cell single nucleotide variation (scSNV) and single-cell copy-number variation (scCNV) data using robust principal component analysis.

Key Features:

• Extended Robust PCA Decomposition: Applies robust principal component analysis (RPCA) for low-rank matrix decomposition to recover true genotype matrices from noisy scSNV and scCNV data.
• Flexible Genotype Encoding: Supports binary (0,1,3) and ternary (0,1,2,3) SNV formats and enables accurate subclonal evolutionary tree reconstruction from recovered genotypes.

Scientific Applications:

• Subclonal Evolution and Tumor Heterogeneity Analysis: Reconstructs clonal genotypes and phylogenetic relationships from single-cell sequencing data to study intratumoral heterogeneity and spatial progression patterns.

Methodology:

RobustClone performs low-rank and sparse matrix decomposition via extended RPCA on scSNV and scCNV genotype matrices, corrects noise and missing values, and infers subclonal evolutionary trees based on the recovered genotype profiles.