Haplotype-aware CNV analysis from single-cell RNA-seq

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.

TarCA is an R package used for inferring the number of progenitors of the focal cell population based on the cell phylogeny.

Calculation of clonality (distances) based on color profiles (Saturation, Hue, and Lightness values)

Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning

LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data

Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations

HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings

Analyses of Penter, Borji & Nagler et al., 2023

Easy-to-use C++ library for the live tracking of lineage and coalescence trees in individual-based forward-in-time simulations.