Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: yurouwang-rosie
- License: mit
- Language: Python
- Default Branch: main
- Size: 44.9 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
InterVelo
Discription
InterVelo is a python package that simultaneously learns cellular pseudotime and RNA velocity. RNA velocity plays a crucial role in uncovering cellular trajectory and genetic transcriptional dynamics from snapshot single-cell data. However, existing RNA velocity inference methods often assume constant transcriptional rates and treat genes independently, which can introduce biases and deviate from biological realities. To address these limitations, we have proposed InterVelo, a novel framework that simultaneously learns cellular pseudotime and RNA velocity. InterVelo uses estimated pseudotime to guide RNA velocity inference and leverages the inferred RNA velocity to refine pseudotime estimation.
Installation
Clone this repository and install it via pip:
bash
git clone https://github.com/yurouwang-rosie/InterVelo.git
cd InterVelo
pip install .
Example
For detailed examples, please refer to the "example" folder.
Owner
- Name: Yurouwang
- Login: yurouwang-rosie
- Kind: user
- Company: Shanghai Jiaotong University
- Repositories: 1
- Profile: https://github.com/yurouwang-rosie
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this code, please cite it as below."
title: " InterVelo: A Mutually Enhancing Model for Estimating Pseudotime and RNA Velocity in Multi-Omic Single-Cell Data"
version: "0.1.1"
doi: "10.5281/zenodo.15876570"
date-released: 2024-07-14
authors:
- family-names: Wang
given-names: Yurou
orcid: https://orcid.org/0009-0002-9394-9858
repository-code: https://github.com/yurouwang-rosie/InterVelo
url: https://doi.org/10.5281/zenodo.15876570
license: MIT
GitHub Events
Total
- Release event: 1
- Public event: 2
- Push event: 5
- Create event: 1
Last Year
- Release event: 1
- Public event: 2
- Push event: 5
- Create event: 1
Dependencies
- numpy *
- requests *
- anndata *
- numpy *
- scvelo *
- torch *