lineage-tracing

There are 14 repositories under lineage-tracing topic.

  • kharchenkolab/numbat

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

    Language:R172919123

  • YosefLab/Cassiopeia

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

    Language:Python83137825

  • chenweng1991/redeemR

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

    Language:Jupyter Notebook133175

  • shadowdeng1994/TarCA

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

    Language:R8103

  • raphael-group/LAML

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

    Language:Python690

  • asalavaty/AutoClone

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

    Language:R2100

  • scDiffEq/LARRY-dataset

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

    Language:Jupyter Notebook2220

  • YosefLab/treedata

    anndata with trees

    Language:Python2502

  • caravagnalab/lineaGT

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

    Language:R130
  • puutools

    charlesrocabert/puutools

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

    Language:C++0300

  • liviuspenter/ONT-lineage-tracing

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

    Language:R0200

  • YosefLab/pycea

    scverse lineage tracing analysis toolkit

    Language:Python0400

  • gil2rok/heracles

    HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings

    10

  • seidels/sciphy-materials

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

    Language:R