{"id":13763676,"url":"https://github.com/vanheeringen-lab/seq2science","last_synced_at":"2025-08-21T01:32:19.529Z","repository":{"id":37090661,"uuid":"196379320","full_name":"vanheeringen-lab/seq2science","owner":"vanheeringen-lab","description":"Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data. 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Please take a look at our [docs](https://vanheeringen-lab.github.io/seq2science/) for help with installation, how to run it, and best practices.\n\n![alt text](https://vanheeringen-lab.github.io/seq2science/_static/seq2science.png \"seq2science\")\n\nOur supported workflows:\n* [Downloading of fastq](https://vanheeringen-lab.github.io/seq2science/content/workflows/download_fastq.html)\n* [Alignment](https://vanheeringen-lab.github.io/seq2science/content/workflows/alignment.html)\n* [ATAC-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/atac_seq.html)\n* [RNA-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html)\n* [ChIP-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/chip_seq.html)\n* [scATAC-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/scatac_seq.html)\n* [scRNA-seq](https://vanheeringen-lab.github.io/seq2science/content/workflows/scrna_seq.html)\n\n## New users\nInformation for new users, such as how to install and configure can be found in our [getting started](https://vanheeringen-lab.github.io/seq2science/content/gettingstarted.html) page, and our [Frequently Asked Questions (FAQ)](https://vanheeringen-lab.github.io/seq2science/content/faq.html) section. \n\n## Feedback\nAnything not working as expected? Please reach out to us via our [issues](https://github.com/vanheeringen-lab/seq2science/issues) page and we'll try to help you as soon as possible!\n\n## Cite us\nvan der Sande M, Frölich S, Schäfers T, Smits JGA, Snabel RR, Rinzema S, van Heeringen SJ. 2023. Seq2science: an end-to-end workflow for functional genomics analysis. PeerJ 11:e16380 https://doi.org/10.7717/peerj.16380\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanheeringen-lab%2Fseq2science","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvanheeringen-lab%2Fseq2science","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvanheeringen-lab%2Fseq2science/lists"}