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

HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings

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

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

Analyses of Penter, Borji & Nagler et al., Nature Communications 2024

Mapping zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a 3-cell rule of branching

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

Here, we publish all scripts to reproduce the analyses in the manuscript Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data

Agent-based LoxCode embryo simulator. Simulates lineage from the 4-cell stage, applies time-windowed loxP barcoding (inversion/excision), and assigns tissue fates via a probabilistic transition matrix. Numba-accelerated, parallel, outputs CSVs, supports CoSpar fate coupling, and R heatmaps.

A Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

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

86% faster data lineage tracking for pandas DataFrames with zero infrastructure. Real-time monitoring, ML anomaly detection, and enterprise compliance features.

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

scverse lineage tracing analysis toolkit

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

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

anndata with trees