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.

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

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

HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings

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

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

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

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

scverse lineage tracing analysis toolkit

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

anndata with trees

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

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

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

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

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