hicream: HI-C diffeREntial Analysis Method
Perform Hi-C data differential analysis based on pixel-level differential analysis and a post hoc inference strategy to quantify signal in clusters of pixels. Clusters of pixels are obtained through a connectivity-constrained two-dimensional hierarchical clustering.
| Version: | 0.0.1 |
| Depends: | R (≥ 4.0.0), reticulate |
| Imports: | adjclust, auk, BiocGenerics, csaw, diffHic, dplyr, edgeR, GenomeInfoDb, GenomicRanges, InteractionSet, limma, Matrix, methods, reshape2, rlang, S4Vectors, stats, SummarizedExperiment, utils, viridis |
| Suggests: | knitr, rmarkdown |
| Published: | 2025-07-25 |
| DOI: | 10.32614/CRAN.package.hicream |
| Author: | Elise Jorge [aut, cre],
Sylvain Foissac [aut],
Pierre Neuvial 
[aut],
Nathalie Vialaneix
[aut],
Gilles Blanchard [ctb],
Guillermo Durand
[ctb],
Nicolas Enjalbert-Courrech [ctb],
Etienne Roquain [ctb] |
| Maintainer: | Elise Jorge <elise.jorge at inrae.fr> |
| BugReports: | https://forgemia.inra.fr/scales/hicream/-/issues |
| License: | GPL (≥ 3) |
| URL: | https://forgemia.inra.fr/scales/hicream |
| NeedsCompilation: | no |
| SystemRequirements: | Python (>= 3.9) |
| Materials: | README |
| CRAN checks: | hicream results |
Documentation:
| Reference manual: | hicream.html , hicream.pdf |
| Vignettes: |
Installation instructions for hicream (source, R code) Introduction to hicream (source, R code) |
Downloads:
| Package source: | hicream_0.0.1.tar.gz |
| Windows binaries: | r-devel: hicream_0.0.1.zip, r-release: hicream_0.0.1.zip, r-oldrel: hicream_0.0.1.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
Linking:
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