lineage-tracing
There are 13 repositories under lineage-tracing topic.
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
YosefLab/Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
chenweng1991/redeemR
R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
shadowdeng1994/TarCA
TarCA is an R package used for inferring the number of progenitors of the focal cell population based on the cell phylogeny.
asalavaty/AutoClone
Calculation of clonality (distances) based on color profiles (Saturation, Hue, and Lightness values)
raphael-group/LAML
LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
scDiffEq/LARRY-dataset
Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning
caravagnalab/lineaGT
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
YosefLab/treedata
anndata with trees
charlesrocabert/puutools
Easy-to-use C++ library for the live tracking of lineage and coalescence trees in individual-based forward-in-time simulations.
liviuspenter/ONT-lineage-tracing
Analyses of Penter, Borji & Nagler et al., 2023
gil2rok/heracles
HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings
YosefLab/pycea
scverse lineage tracing analysis toolkit