A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
☆99Feb 5, 2026Updated last month
Alternatives and similar repositories for Cassiopeia
Users that are interested in Cassiopeia are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Lineage Tracing by Integrating Mutation and Transcriptomic data☆13Jun 16, 2020Updated 5 years ago
- Code & utilities for the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"☆14May 27, 2023Updated 2 years ago
- ☆10Sep 27, 2022Updated 3 years ago
- Reproducing the experiments in the paper☆11Dec 14, 2021Updated 4 years ago
- ☆10Oct 15, 2025Updated 5 months ago
- ☆33Mar 16, 2026Updated last week
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆43Sep 18, 2025Updated 6 months ago
- ☆13Jul 28, 2023Updated 2 years ago
- ☆11Feb 11, 2021Updated 5 years ago
- Collection of code for the GESTALT fate mapping paper using the CRISPR/Cas9 system☆25Jan 8, 2018Updated 8 years ago
- ☆26Dec 25, 2023Updated 2 years ago
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆22Jun 10, 2022Updated 3 years ago
- ☆12Apr 16, 2021Updated 4 years ago
- Updated scripts and pipelines for processing GESTALT data at single-cell resolution☆20May 22, 2021Updated 4 years ago
- CellPhy: accurate and fast probabilistic inference of single-cell phylogenies☆20Jan 8, 2026Updated 2 months ago
- Code repository for macsGESTALT single cell lineage tracing analysis https://doi.org/10.1101/2020.08.11.245787☆10May 10, 2021Updated 4 years ago
- This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…☆26Oct 17, 2024Updated last year
- 🦀 Tumor growth simulation in C++/R☆20Dec 30, 2025Updated 2 months ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆21Jul 13, 2023Updated 2 years ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Jan 15, 2020Updated 6 years ago
- CellRank: dynamics from multi-view single-cell data☆433Mar 9, 2026Updated 2 weeks ago
- ☆145Apr 19, 2025Updated 11 months ago
- Reproducing all analyses and figures for the ASAP-seq paper☆29Jun 11, 2021Updated 4 years ago
- This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expressio…☆28Dec 1, 2025Updated 3 months ago
- Dynamical systems methods for RNA velocity analysis☆24May 19, 2021Updated 4 years ago
- FRACTAL: framework for distributed computing to trace large accurate lineages☆24Sep 6, 2022Updated 3 years ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆488Updated this week
- Reference mapping for single-cell genomics☆400Dec 2, 2025Updated 3 months ago
- Code, data and analysis for moslin.☆15Oct 7, 2024Updated last year
- mgatk: mitochondrial genome analysis toolkit☆111Jan 20, 2025Updated last year
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆207Feb 4, 2026Updated last month
- 𝒫robabilistic modeling of RNA velocity ⬱☆49Updated this week
- PRObabilistic Simulations of ScRNA-seq Tree-like Topologies☆26Jan 10, 2024Updated 2 years ago
- SCOUP is a probabilistic model to analyze single-cell expression data during differentiation☆10Apr 20, 2017Updated 8 years ago
- Integrating temporal gene expression modalities for trajectory inference and disease prediction☆10Sep 20, 2022Updated 3 years ago
- Template repository for creating novel models with scvi-tools☆20Jan 18, 2023Updated 3 years ago
- Single cell trajectory detection☆298Feb 14, 2026Updated last month
- UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference☆27Nov 12, 2024Updated last year
- ☆25Mar 3, 2020Updated 6 years ago