{"repo":"epigen/rnaseq_pipeline","free":true,"listed":false,"github":"https://github.com/epigen/rnaseq_pipeline","clone":"git clone https://github.com/epigen/rnaseq_pipeline.git","description":"RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.","language":"Python","stars":46,"topics":["bash","bioinformatics","biomedical-data-science","ngs","pipeline","python","rna-seq","rna-seq-pipeline","rnaseq","snakemake"],"license":"MIT","category":"cli-tools","readme_excerpt":"RNA-seq Data Processing, Quantification & Annotation Pipeline A Snakemake workflow for end-to-end processing, quantification, and annotation of gene expression for RNA-seq experiments, starting from single- or paired-end reads within raw/unaligned/unmapped uBAM files, including a comprehensive MultiQC report. [!NOTE] This workflow adheres to the module specifications of MrBiomics, an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository. ⭐️ Star and share modules you find valuable 📤 - help others discover them, and guide our future work! [!IMPORTANT] If you use this workflow in a publication, please don't forget to give credit to the authors by citing it using this DOI 10.5281/zenodo.15119355 and acknowledge the rna-seq-star-deseq2 workflow DOI 10.5281/zenodo.4737358 from which some structure and code were adapted. 🖋️ Authors - Stephan Reichl - Raphael Bednarsky - Jake Burton - Fangwen Zhao - Lina Dobnikar - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies. Software Reference (DOI / URL) :-------------------: :-----------------------------------------------: Snakemake https://doi.org/10.12688/f1000research.29032.2 STAR https://doi.org/10.1093/bioinformatics/bts635 Samtools https://doi.org/10.1093/bioinformatics/btp352 MultiQC https://doi.org/10.1093/bioinformatics/btw354 RSeQC https://doi.org/10.1093/bioinformatics/","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/rnaseq_pipeline/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}