graph_distances
Codebase for computing distances between lineage trees
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (5.5%) to scientific vocabulary
Repository
Codebase for computing distances between lineage trees
Basic Info
- Host: GitHub
- Owner: shahlab-ucla
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Size: 20.7 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 4
Metadata Files
README.md
graph_distances
Codebase for computing distances between lineage trees described in our preprint: https://www.biorxiv.org/content/10.1101/2023.05.12.540617v1
Listed below are jupyter notebooks used to generate the data necessary to reproduce each of the main and supplemental figures for the publication. The main and supplemental figures are produced by distinct notebooks, each with different parent folders and input data. (due to distinct file pathing requirements)
These notebooks, if put into the appropriate environments and run, will produce the requisite data/plots to recreate the figures of the paper. All computational analyses were completed with python, and figures were made in python and MATLAB. Some aesthetic details of the figures were modified by editing scalable vector graphics exported from the data generated using this code, however the underlying data is identical.
Raw lineage data was procured from http://digital-development.org/ and was initially described in this publication: Du, Z, Santella, A, He, F, Shah, PK, Kamikawa, Y and Bao, Z. (2015). The regulatory landscape of lineage differentiation in a Metazoan embryo. Developmental Cell, 34(5), 592-607.
Owner
- Login: shahlab-ucla
- Kind: user
- Repositories: 1
- Profile: https://github.com/shahlab-ucla
Citation (CITATION.cff)
ff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: Natesan given-names: Gunalan - family-names: Hamilton given-names: Timothy - family-names: Deeds given-names: Eric J - family-names: Shah given-names: Pavak K title: Graph_distances version: 1.1.0 date-released: 2023-11-14 url: https://github.com/shahlab-ucla/graph_distances