R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
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Updated
Jul 16, 2024 - Jupyter Notebook
R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
anndata with trees
LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
Haplotype-aware CNV analysis from single-cell RNA-seq
scverse lineage tracing analysis toolkit
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Easy-to-use C++ library for the live tracking of lineage and coalescence trees in individual-based forward-in-time simulations.
Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning
TarCA is an R package used for inferring the number of progenitors of the focal cell population based on the cell phylogeny.
Analyses of Penter, Borji & Nagler et al., 2023
HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings
Calculation of clonality (distances) based on color profiles (Saturation, Hue, and Lightness values)
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