shaman: Sampling Hi-C Contact Matrices for Aparametric Normalization

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 [issues need fixing before 2026-11-06]

Documentation:

Reference manual:	shaman.html , shaman.pdf
Vignettes:	Import (source, R code) The shaman package - Sampling HiC contAct Matrices for Aparametric Normalization (source)

Downloads:

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): shaman_2.1.0.tgz, r-oldrel (arm64): shaman_2.1.0.tgz, r-release (x86_64): shaman_2.1.0.tgz, r-oldrel (x86_64): shaman_2.1.0.tgz

Linking:

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