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.
Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning
scverse lineage tracing analysis toolkit
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
Easy-to-use C++ library for the live tracking of lineage and coalescence trees in individual-based forward-in-time simulations.
Cell lineage analysis for timelapse microscopy. Build one spatiotemporal graph tracking cell lineage and spatial neighbours together, easily handling large and complex datasets.
Analysis code for the MetTag lineage-barcoding study of TNBC lung metastasis (accompanies manuscript; GEO: GSE309120)
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.
HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings
Thymic NK-cell development — single-cell mtDNA clonal lineage tracing (mgatk/ReDeeM), clone inference and HPC pipelines
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