https://github.com/pinellolab/stream2
STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
https://github.com/pinellolab/stream2
Last synced: 11 months ago
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STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
- Host: GitHub
- URL: https://github.com/pinellolab/stream2
- Owner: pinellolab
- License: bsd-3-clause
- Created: 2021-01-15T01:58:44.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-04-01T17:31:36.000Z (about 2 years ago)
- Last Synced: 2025-06-07T04:07:42.184Z (about 1 year ago)
- Language: Python
- Homepage: https://stream-bio.readthedocs.io
- Size: 4.29 MB
- Stars: 10
- Watchers: 4
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://github.com/pinellolab/stream2/actions/workflows/CI.yml)
# STREAM2
STREAM2 (**S**ingle-cell **T**rajectories **R**econstruction, **E**xploration **A**nd **M**apping) is an interactive pipeline capable of disentangling and visualizing complex trajectories from for single-cell omics data.
Installation
------------
```sh
$ pip install git+https://github.com/pinellolab/STREAM2
```
Tutorials
---------
Preliminary tutorials for the usage of STREAM2 can be found at **STREAM2_tutorials** repository https://github.com/pinellolab/STREAM2_tutorials.
Description
-----------
The four key innovations of STREAM2 are:
1) STREAM2 can learn more biologically meaningful trajectories in a semi-supervised way by leveraging external information (e.g. time points, FACS labels, predefined relations of clusters, etc.);
2) STREAM2 is able to learn not only linear or tree-like structures but also more complex graphs with loops or disconnected components;
3) STREAM2 supports trajectory inference for various single-cell assays such as gene expression, chromatin accessibility, protein expression level, and DNA methylation;
4) STREAM2 introduces a flexible path-based marker detection procedure. In addition, we provide a scalable and fast python package along with a comprehensive documentation website to facilitate STREAM2 analysis.
