Work

Inference of single-cell phylogenies from lineage tracing data with Cassiopeia

Year: 2020

Type: dataset

Abstract: Synthetic benchmarking data used in our study entitled "Inference of single-cell phylogenies from lineage tracing data with Cassiopeia" published in Genome Biology. Phylogenies were simulated with varying characters, states, experimental durations, mutation rates, dropout rates, and state distributions as described in our manuscript. This dataset includes simulated phylogenies of size 400 and 1000 cells. Each phylogeny is saved as a python Networkx object, pickled for convenience. These objects can be read in using Python version >= 3 with the "pickle" library. For stress testing and simulating additional phylogenies, please refer to our Github: https://github.com/YosefLab/Cassiopeia

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.3706350

Authors: Jones, Matthew G, Khodaverdian, Alex, Quinn, Jeffrey J, Chan, Michelle M, Hussmann, Jeffrey A, Wang, Robert, Chenling Xu, Weissman, Jonathan S, Yosef, Nir

Institutions: University of California, San Francisco, University of California, Berkeley

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W4393701989

Cites:

Cited by: 1

Related to: 10