https://github.com/chelauk/liqa
Long-read Isoform Quantification and Analysis
Science Score: 23.0%
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Low similarity (8.9%) to scientific vocabulary
Last synced: 9 months ago
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Long-read Isoform Quantification and Analysis
Basic Info
- Host: GitHub
- Owner: chelauk
- License: other
- Default Branch: master
- Size: 3.1 MB
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- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of WGLab/LIQA
Created over 4 years ago
· Last pushed over 4 years ago
https://github.com/chelauk/LIQA/blob/master/
# Long-read Isoform Quantification and Analysis [](https://zenodo.org/badge/latestdoi/257630000) LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads instead of summarizing isoform-specific read counts directly. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates. ## Computational pipeline of LIQA## Inputs of LIQA The input of LIQA is long-read RNA-seq read data in BAM format together with a refrence isoform annotation file. ## Installation Please refer to [Installation](https://github.com/WGLab/LIQA/blob/master/doc/Install.md) for how to install LIQA. ## Usage Please refere to [Usage](https://github.com/WGLab/LIQA/blob/master/doc/Usage.md) for how to use LIQA. ## Examples of isoform analysis using LIQA. Please refer to [Demo and Examples](https://github.com/WGLab/LIQA/blob/master/doc/Examples.md) for examples of how to use LIQA. ## Contact If you have any questions/issues/bugs, please post them on [GitHub](https://github.com/WGLab/LIQA/issues). They would also be helpful to other users. ## Citation Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang. LIQA: Long-read Isoform Quantification and Analysis. 2020. bioRxiv doi: [https://doi.org/10.1101/2020.09.09.289793](https://www.biorxiv.org/content/10.1101/2020.09.09.289793v1)
Owner
- Name: Chela James
- Login: chelauk
- Kind: user
- Location: Milan
- Company: Fondazione Human Technopole
- Website: http://www.sottorivalab.org/
- Twitter: chelauk
- Repositories: 61
- Profile: https://github.com/chelauk
Senior Bioinformatician Fondazione Human Technopole