GitHub topics: lineage-tracing
caravagnalab/lineaGT
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
Language: R - Size: 20 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 0
chenweng1991/redeemR
R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
Language: Jupyter Notebook - Size: 17.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 13 - Forks: 5
YosefLab/treedata
anndata with trees
Language: Python - Size: 614 KB - Last synced at: about 3 hours ago - Pushed at: about 4 hours ago - Stars: 3 - Forks: 3
YosefLab/pycea
scverse lineage tracing analysis toolkit
Language: Python - Size: 601 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 1
YosefLab/Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Language: Python - Size: 46 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 86 - Forks: 28
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language: R - Size: 390 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 180 - Forks: 23
raphael-group/LAML
LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
Language: Python - Size: 59.5 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 6 - Forks: 1
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 - Size: 26.6 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
liviuspenter/ONT-lineage-tracing
Analyses of Penter, Borji & Nagler et al., Nature Communications 2024
Language: R - Size: 60.4 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
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: R - Size: 693 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 2
scDiffEq/LARRY-dataset
Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning
Language: Jupyter Notebook - Size: 7.42 MB - Last synced at: 11 months ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0
gil2rok/heracles
HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings
Size: 19.5 KB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
asalavaty/AutoClone
Calculation of clonality (distances) based on color profiles (Saturation, Hue, and Lightness values)
Language: R - Size: 2 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
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++ - Size: 7.85 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
