lineage-tracing

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

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.

Reconstructing single-cell lineage history using mitochondrial mutation drift dynamics

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

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

anndata with trees

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

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

scverse lineage tracing analysis toolkit

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

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

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

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

Cell lineage analysis for timelapse microscopy. Build one spatiotemporal graph tracking cell lineage and spatial neighbours together, easily handling large and complex datasets.

Biohub - Cell Tracking During Development (Kaggle 2026, team InSociEUP): own 3D detector/linker, 22 leaderboard probes on the public tracking pipeline, metric notes. Private LB 0.921, rank 288/4020.

Analysis code for the MetTag lineage-barcoding study of TNBC lung metastasis (accompanies manuscript; GEO: GSE309120)

Fitness-adjusted evaluation of pre-treatment cell fate prediction from sister-cell lineage tracing (single-cell RNA-seq)

Lineage-aware single-cell dynamics in split latent spaces with identity-locked neural ODEs and clone-aware optimal transport.