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 to download and view the source code

Also see the Swan manuscript repository for the exact commands used to do the analysis in our publication.

Also see our website 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, moving to the swan_vis directory, and running

pip install .

Tutorials

• Data preprocessing with TALON
• Getting started: how to load data into Swan
• Visualization tools: make gene and transcript-level plots to visualize the complexity of alternative splicing
• Analysis tools: find differentially expressed genes and transcripts; find isoform-switching genes, discover novel intron retention and exon skipping events
• Scanpy compatibility: Some brief examples of how to use external Scanpy plotting functions on Swan objects

FAQs

• Understanding Swan visualizations
• Additional utilities
• SwanGraph data structure
• Input file format specifications

Comprehensive Documentation

For full documentaion, please visit our website

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