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.

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

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

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

anndata with trees

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

scverse lineage tracing analysis toolkit

HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings

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

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