README.md

# Replication repository for the article "A comprehensive review and benchmark of differential analysis tools for Hi-C data"

Scripts and their outputs are available in directory `scripts` (numbered by their order of dependency). They require data that can be downloaded at https://doi.org/10.57745/LR0W9R. The CTCF scripts additionally require the file obtained at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129997 `GSE129997_CTCF_midG1.narrowPeak.gz` (CTCF occupancy obtained by ChIP-Seq experiment on a murine cell line [Zhang *et al.*, 219]; to be uncompressed and placed in `data/ctcf/100000`). The files `load_modules*` give information about software requirements and the file `renv.lock` information about used **R** packages (to be used with the **R** package `renv`). 

**Important note**: The **R** package `FIND` is not available for direct installation from a standard repository (CRAN or Bioconductor) and has to be manually installed from its source repository https://bitbucket.org/nadhir/find. We advise that:
- You comment the entry corresponding to `FIND` in `renv.lock`;
- You restore the current repository from `renv.lock` using `renv`;
- You install `FIND` from its source repository.

## Authors and citation

Élise Jorge, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet-Tolosan, France

Sylvain Foissac, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet-Tolosan, France

Pierre Neuvial, Institut de Mathématiques de Toulouse, UMR 5219, Université de Toulouse, CNRS UPS, 31062 Toulouse, France

Matthias Zytnicki, Université Fédérale de Toulouse, INRAE, MIAT, 31326 Castanet-Tolosan, France

Nathalie Vialaneix, Université Fédérale de Toulouse, INRAE, MIAT, 31326 Castanet-Tolosan, France

For information about the repository, please contact celine.brouard@inrae.fr or nathalie.vialaneix@inrae.fr.

Citation will be made available when the article is published.

## License

The content of this repository is released under GPL v3 (or later).

## References

Haoyue Zhang, Daniel J. Emerson, Thomas G. Gilgenast, Katelyn R. Titus, Yemin Lan, Peng Huang, Di Zhang, Hongxin Wang, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, Jennifer E. Phillips-Cremins, and Gerd A. Blobel. Chromatin structure dynamics during the mitosis-to-g1 phase transition. *Nature*, 576(7785):158–162, November 2019.