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.