Add https://github.com/LaureTomas/HiCaptuRe/

README.md

@@ -1355,7 +1355,7 @@ Tools are added by publication date, newest on top. Unpublished tools are listed
 
 - [4D Nucleome Protocols](https://www.4dnucleome.org/protocols.html) - Collection of genomic technologies currently in use or being developed in the 4DN network - links to wet-lab protocols and papers. [4DN portal blog](https://www.4dnucleome.org/outreach.html)
 
-- [liCHi-C](https://github.com/JavierreLab/liCHiC) - low input capture Hi-C technology (above 50K cells in contrast to 30-50M cells for promoter-capture). Developed for promoter capture but can be adapted to any capture regions. HiCUP pipeline, CHiCAGO to detect significant interactions, HICCUPS, Mustache and HiCExplorer to call loops on Knight-Ruiz normalized matrices at 5kb resolution. Applied to normal and malignant human hematopoietic hierarchy in clinical samples, reconstructs lineages. Benchmarked against Low-C, Hi-C with different restriction enzymes, TagHi-C. Can be used to detect structural variants, breakpoints, link disease variants to genes. [Data](https://ega-archive.org/studies/EGAS00001006305), scripts and processed data on [Zenodo](https://zenodo.org/record/7351026). Additional software: [CHIGP](https://github.com/ollyburren/CHIGP) R package for integrating GWAS summary statistics with CHiCAGO output, poor man's imputation algorithm for GWAS, Blockshifter, COGS. [RegioneReloaded](https://bioconductor.org/packages/regioneReloaded/) - Bioconductor package for comparative permutation analysis of multiple genomic region sets. See also the [promoter-capture PCHi-C paper](https://github.com/mdozmorov/HiC_data#phic). [GitHub](https://github.com/JavierreLab/liCHiC/tree/main). <details>
+- [liCHi-C](https://github.com/JavierreLab/liCHiC) - low input capture Hi-C technology (above 50K cells in contrast to 30-50M cells for promoter-capture). Developed for promoter capture but can be adapted to any capture regions. HiCUP pipeline, CHiCAGO to detect significant interactions, HICCUPS, Mustache and HiCExplorer to call loops on Knight-Ruiz normalized matrices at 5kb resolution. Applied to normal and malignant human hematopoietic hierarchy in clinical samples, reconstructs lineages. Benchmarked against Low-C, Hi-C with different restriction enzymes, TagHi-C. Can be used to detect structural variants, breakpoints, link disease variants to genes. [Data](https://ega-archive.org/studies/EGAS00001006305), scripts and processed data on [Zenodo](https://zenodo.org/record/7351026). Additional software: [CHIGP](https://github.com/ollyburren/CHIGP) R package for integrating GWAS summary statistics with CHiCAGO output, poor man's imputation algorithm for GWAS, Blockshifter, COGS. [RegioneReloaded](https://bioconductor.org/packages/regioneReloaded/) - Bioconductor package for comparative permutation analysis of multiple genomic region sets. [HiCaptuRe](https://github.com/LaureTomas/HiCaptuRe/) - R package for Capture Hi-C data management, handles CHiCAGO output. See also the [promoter-capture PCHi-C paper](https://github.com/mdozmorov/HiC_data#phic). [GitHub](https://github.com/JavierreLab/liCHiC/tree/main). <details>
   <summary>Paper</summary>
   Tomás-Daza, Laureano, Llorenç Rovirosa, Paula López-Martí, Andrea Nieto-Aliseda, François Serra, Ainoa Planas-Riverola, Oscar Molina, et al. “Low Input Capture Hi-C (LiCHi-C) Identifies Promoter-Enhancer Interactions at High-Resolution.” Nature Communications 14, no. 1 (January 17, 2023): 268. https://doi.org/10.1038/s41467-023-35911-8.
 </details>