{"id":50445496,"url":"https://github.com/sebastian-gregoricchio/snhic","last_synced_at":"2026-05-31T21:02:57.354Z","repository":{"id":63579071,"uuid":"476682447","full_name":"sebastian-gregoricchio/snHiC","owner":"sebastian-gregoricchio","description":"Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. 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The input files required to run the pipeline are Paired-End fastq files. The pipeline performs data quality control, normalization and correction. It also includes the possibility to perform grouped analyses (e.g, merging of replicates) besides TAD, loops and stripes detection and differential contacts and compartment analyses. Notabily, the latter is performed using `dcHiC`, a recently published method ([A. Chakraborty, *et al.*, Nat. Comm. 2022](https://www.nature.com/articles/s41467-022-34626-6)) that enables more precise and high-resolution differential compartment analyses.\r\n\r\n\r\n### Citation\r\nIf you use this pipeline, please cite:\r\n\r\n\u003cdiv class=\"warning\" style='padding:2.5%; background-color:#ffffee; color:#787878; margin-left:5%; margin-right:5%; border-radius:15px;'\u003e\r\n\u003cspan\u003e\r\n\u003cfont size=\"-0.5\"\u003e\r\n\r\n\u003cdiv style=\"margin-left:2%; margin-right:2%; text-align: justify\"\u003e\r\nS. Gregoricchio \u0026 W. Zwart. \"\u003ci\u003esnHiC\u003c/i\u003e: a complete and simplified snakemake pipeline for grouped Hi-C data analysis\". \u003cbr\u003e\r\n\u003ci\u003eBioinformatics Adavances\u003c/i\u003e, Volume 3, Issue 1, 2023, vbad080 \u003cbr\u003e\r\nDOI: \u003ca href=\"https://doi.org/10.1093/bioadv/vbad080\"\u003e10.1093/bioadv/vbad080\u003c/a\u003e\r\n\u003c/div\u003e\r\n\u003c/font\u003e\r\n\r\n\u003c/span\u003e\r\n\u003c/div\u003e\r\n\r\n\u003cbr/\u003e\u003cbr/\u003e\r\n\r\n## Documentation [\u003cimg src=\"https://raw.githubusercontent.com/sebastian-gregoricchio/sebastian-gregoricchio.github.io/main/generic_resources/documentation.svg\" align=\"right\" height = 150/\u003e](https://github.com/sebastian-gregoricchio/snHiC/wiki)\r\nDetails on the [installation](https://github.com/sebastian-gregoricchio/snHiC/wiki/2.-Installation-and-dependencies) and [usage](https://github.com/sebastian-gregoricchio/snHiC/wiki/3.-Run-the-pipeline) of snHiC can be found at the dedicated [Wiki](https://github.com/sebastian-gregoricchio/snHiC/wiki/).\r\n\r\n\u003cbr/\u003e\u003cbr/\u003e\r\n\r\n-----------------\r\n## Package history and releases\r\nA list of all releases and respective description of changes applied could be found [here](https://sebastian-gregoricchio.github.io/snHiC/NEWS).\r\n\r\n## Contact\r\nFor any suggestion, bug fixing, commentary please report it in the [issues](https://github.com/sebastian-gregoricchio/snHiC/issues)/[request](https://github.com/sebastian-gregoricchio/snHiC/pulls) tab of this repository.\r\n\r\n## License\r\nThis repository is under a [GNU General Public License (version 3)](https://sebastian-gregoricchio.github.io/snHiC/LICENSE.md/LICENSE).\r\n\r\n\u003cbr/\u003e\r\n\r\n#### Contributors\r\n[![contributors](https://contrib.rocks/image?repo=sebastian-gregoricchio/snHiC)](https://sebastian-gregoricchio.github.io/)\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastian-gregoricchio%2Fsnhic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsebastian-gregoricchio%2Fsnhic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastian-gregoricchio%2Fsnhic/lists"}