Generate expected Hi-C (genome-wide chromosome conformation capture) data maintaining marginal coverage, and the decay in contact probability with increasing genomic distance. Expected Hi-C data is used for normalization and graphical presentation of statistical significance of observed Hi-C contact enrichments. The method is described in Mendelson Cohen et al. (2017) <doi:10.1101/187203>.
| Version: | 2.1.0 |
| Depends: | R (≥ 4.0.0) |
| Imports: | misha (≥ 3.5.6), Rcpp (≥ 0.12.11), RANN, data.table, ggplot2 (≥ 3.4.0), reshape2, grid, plyr, parallel |
| LinkingTo: | Rcpp |
| Suggests: | knitr, testthat, rmarkdown, Gviz, foreach |
| OS_type: | unix |
| Published: | 2026-10-16 |
| DOI: | 10.32614/CRAN.package.shaman (may not be active yet) |
| Author: | Amos Tanay [aut], Netta Mendelson Cohen [aut], Aviezer Lifshitz [aut, cre], Weizmann Institute of Science [cph] |
| Maintainer: | Aviezer Lifshitz <aviezer.lifshitz at weizmann.ac.il> |
| BugReports: | https://github.com/tanaylab/shaman/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL] |
| URL: | https://tanaylab.github.io/shaman/, https://github.com/tanaylab/shaman |
| NeedsCompilation: | yes |
| SystemRequirements: | C++17 |
| Citation: | shaman citation info |
| Materials: | README, NEWS |
| CRAN checks: | shaman results |
| Reference manual: | shaman.html , shaman.pdf |
| Vignettes: |
Import (source, R code) The shaman package - Sampling HiC contAct Matrices for Aparametric Normalization (source) |
| Package source: | shaman_2.1.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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