├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── img └── 3C_technologies.png ├── pipeline_comparison.csv └── pipelines_list.csv /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing 2 | 3 | Please, help with the [Issue #6: Add Altmetrics badges to each paper](https://github.com/mdozmorov/HiC_tools/issues/6) 4 | 5 | Your contributions are always welcome! 6 | 7 | * Open an issue with any suggestion/correction 8 | * Send a Pull Request 9 | * Contact me on Twitter @mikhaildozmorov or by e-mail mikhail.dozmorov@gmail.com 10 | 11 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Mikhail Dozmorov 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /img/3C_technologies.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/HiC_tools/7d950745df31f499c0f91efac9f8cae30c4d65c9/img/3C_technologies.png -------------------------------------------------------------------------------- /pipeline_comparison.csv: -------------------------------------------------------------------------------- 1 | HiCUP[37],,,,,,,,,,,,, 2 | Language,"Unix, Perl","R, Python",R,"Perl, R",Java,R,"Python, Perl, R",Python,Python,R,"Perl, R",Python,"Perl, Java, R" 3 | Mapping,✓,✓,,✓,✓,✓,✓,✓,✓,✓,,✓, 4 | Filtering,✓,✓,,✓,✓,✓,✓,✓,✓,✓,,✓,✓ 5 | Quality control,✓,✓,✓,✓,✓,✓,✓,✓,✓,✓,,✓,✓ 6 | Contact map,,✓,✓,✓,✓,✓,,✓,✓,✓,✓,✓,✓ 7 | Specific interactions,,,,,✓,✓,✓,,,✓,,,✓ 8 | Allele-specific analysis,✓,✓,,,✓,,,,,,,, 9 | Visualization,,,✓,✓,,✓,,✓,✓,✓,,✓,✓ 10 | A/B compartmentalization,,,,,✓,,,✓,,✓,,✓,✓ -------------------------------------------------------------------------------- /pipelines_list.csv: -------------------------------------------------------------------------------- 1 | Pipeline,URL 2 | HiCUP,https://www.bioinformatics.babraham.ac.uk/projects/hicup/ 3 | HiC-Pro,https://github.com/nservant/HiC-Pro 4 | HiTC,http://bioconductor.org/packages/release/bioc/html/HiTC.html 5 | HiC-inspector,https://github.com/HiC-inspector/HiC-inspector 6 | Juicer,https://github.com/theaidenlab/juicer 7 | HiC-bench,https://github.com/NYU-BFX/hic-bench 8 | HIPPIE,http://wanglab.pcbi.upenn.edu/hippie/ 9 | TADbit,https://github.com/3DGenomes/tadbit 10 | HiFive,https://github.com/bxlab/hifive 11 | HiCdat,https://github.com/MWSchmid/HiCdat 12 | hicpipe,https://compgenomics.weizmann.ac.il/tanay/?page_id=283 13 | hiclib,https://bitbucket.org/mirnylab/hiclib 14 | HOMER,http://homer.ucsd.edu/homer/interactions/index.html --------------------------------------------------------------------------------