GitHub topics: lineage-tracing
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Language: R - Size: 390 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 191 - Forks: 25
ReoNa0216/LoxSimforEmbryo
Agent-based LoxCode embryo simulator. Simulates lineage from the 4-cell stage, applies time-windowed loxP barcoding (inversion/excision), and assigns tissue fates via a probabilistic transition matrix. Numba-accelerated, parallel, outputs CSVs, supports COSPAR fate coupling, and R heatmaps.
Language: Python - Size: 153 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0
YosefLab/pycea
scverse lineage tracing analysis toolkit
Language: Python - Size: 1.83 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1
YosefLab/Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Language: Python - Size: 60.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 90 - Forks: 28
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: 44.5 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0
chenweng1991/redeemR
R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
Language: Jupyter Notebook - Size: 18.5 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 14 - Forks: 5
YosefLab/treedata
anndata with trees
Language: Python - Size: 1010 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 6 - Forks: 3
Locpotter/DataLineagePy
DataLineagePy offers a straightforward way to track data lineage in Python applications. It ensures clear visibility of data flow and transformations, making it essential for data management. 🐙🌐
Language: Python - Size: 498 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
raphael-group/LAML
LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
Language: Python - Size: 59.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 8 - Forks: 1
Arbaznazir/DataLineagePy
86% faster data lineage tracking for pandas DataFrames with zero infrastructure. Real-time monitoring, ML anomaly detection, and enterprise compliance features.
Language: Python - Size: 535 KB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
scDiffEq/LARRY-dataset
Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning
Language: Jupyter Notebook - Size: 7.41 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0
caravagnalab/lineaGT
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
Language: R - Size: 20 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - 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: about 1 year ago - Pushed at: about 1 year 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: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2
giladturok/heracles
HERACLES algorithm reconstructs CRISPR-Cas9 lineages with hyperbolic embeddings
Size: 19.5 KB - Last synced at: 2 days ago - Pushed at: over 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: over 2 years ago - Pushed at: almost 3 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: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
