{"repo":"epigen/atacseq_pipeline","free":true,"listed":false,"github":"https://github.com/epigen/atacseq_pipeline","clone":"git clone https://github.com/epigen/atacseq_pipeline.git","description":"Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.","language":"Python","stars":102,"topics":["snakemake","atac-seq","python","bioinformatics","workflow","ngs","pipeline","biomedical-data-science","bash"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Ultimate ATAC-seq Data Processing, Quantification & Annotation Pipeline A Snakemake 8 workflow implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using Bash and Python. [!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.6323634. 🖋️ Authors - Stephan Reichl - Bekir Ergüner - Daniele Barreca - Lukas Folkman - Fangwen Zhao - Rob ter Horst - Lina Dobnikar - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies: Software Reference (DOI) :------------: :-----------------------------------------------: bedtools https://doi.org/10.1093/bioinformatics/btq033 Bowtie2 https://doi.org/10.1038/nmeth.1923 deeptools https://doi.org/10.1093/nar/gkw257 ENCODE https://doi.org/10.1038/s41598-019-45839-z fastp https://doi.org/10.1093/bioinformatics/bty560 HOMER https://doi.org/10.1016/j.molcel.2010.05.004 MACS2 https://doi.org/10.1186/gb-2008-9-9-r137 MultiQC https://doi.org/10.1093/bioinformatics/btw354 pybedtools https://doi.org/10.1093/bioinfor","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/atacseq_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."}