This repository provides a comprehensive workflow for RNA-seq data analysis, covering everything from upstream data processing to downstream analysis. The workflow includes quality control, read alignment, gene and transcript-level quantification, visualization, differential gene expression analysis, and more. The implementation is based on methodologies described in the following literature:
The workflow is designed to be flexible and customizable, allowing users to choose from multiple algorithms for quality control and read alignment based on their project requirements.
Contributions are welcome! If you have suggestions for improving the workflow or adding new features, please open an issue or submit a pull request.
If you use this workflow in your research, please cite the original paper that inspired this implementation: Conesa, A., Madrigal, P., Tarazona, S. et al. A survey of best practices for RNA-seq data analysis. Genome Biol 17, 13 (2016). https://doi.org/10.1186/s13059-016-0881-8