https://github.com/mortazavilab/swan_vis
A Python library to visualize and analyze long-read transcriptomes
https://github.com/mortazavilab/swan_vis
bioinformatics long-read oxford-nanopore pacbio pacbio-iso-seq transcriptome
Last synced: 3 months ago
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A Python library to visualize and analyze long-read transcriptomes
- Host: GitHub
- URL: https://github.com/mortazavilab/swan_vis
- Owner: mortazavilab
- License: mit
- Created: 2019-11-19T00:26:53.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-05-01T17:45:30.000Z (about 1 year ago)
- Last Synced: 2025-12-16T12:46:54.917Z (6 months ago)
- Topics: bioinformatics, long-read, oxford-nanopore, pacbio, pacbio-iso-seq, transcriptome
- Language: Jupyter Notebook
- Homepage: https://freese.gitbook.io/swan/
- Size: 63.9 MB
- Stars: 64
- Watchers: 3
- Forks: 11
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Swan
Swan is a Python library designed for the analysis and visualization of transcriptomes, especially with long-read transcriptomes in mind. Users can add transcriptomes from different datasets and explore distinct splicing and expression patterns across datasets.
Please visit the [Swan repository](https://github.com/mortazavilab/swan_vis) to download and view the source code
Also see the [Swan manuscript repository](https://github.com/fairliereese/swan_paper) for the exact commands used to do the analysis in our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa836/5912931).
Also see our [website](https://freese.gitbook.io/swan/) for in-depth tutorials and documentation
## What can Swan do?
Swan can make informative plots, find differentially expressed genes and transcripts, find isoform-switching genes, and discover novel exon skipping and intron retention events.
## Installation
Swan can be installed directly from PyPi. To install Swan's most recent release, run
`pip install swan_vis`
Alternatively, the most recent commits can be installed by git cloning [the Swan repository](https://github.com/fairliereese/swan_vis), moving to the swan\_vis directory, and running
`pip install .`
## Tutorials
* [Data preprocessing with TALON](tutorials/data_processing.md)
* [Getting started](tutorials/getting_started.md): how to load data into Swan
* [Visualization tools](tutorials/visualization.md): make gene and transcript-level plots to visualize the complexity of alternative splicing
* [Analysis tools](tutorials/analysis_tools.md): find differentially expressed genes and transcripts; find isoform-switching genes, discover novel intron retention and exon skipping events
* [Scanpy compatibility](tutorials/scanpy_compatibility.md): Some brief examples of how to use external Scanpy plotting functions on Swan objects
## FAQs
* [Understanding Swan visualizations](faqs/understanding_swan_vis.md)
* [Additional utilities](faqs/utilities.md)
* [SwanGraph data structure](faqs/data_structure.md)
* [Input file format specifications](faqs/file_formats.md)
## Comprehensive Documentation
For full documentaion, please visit [our website](https://freese.gitbook.io/swan/)
Logo by the wonderful [Eamonn Casey](https://www.instagram.com/designsbyeamonn/)