Package: CALDER
Type: Package
Title: CALDER: a Hi-C analysis tool for inferring non-linear hierarchical organization of the 3D chromosome
Version: 2.0
Date: 2022-05-10
Author: Yuanlong LIU
Maintainer: Who to complain to <yliueagle@googlemail.com>
Description: CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each chromatin domain from short-range contacts
LinkingTo: Rcpp, RcppArmadillo
Authors@R: c(
    person(given = "Yuanlong",
           family = "LIU",
           role = c("aut", "cre"),
           email = "yliueagle@googlemail.com"))
URL: https://github.com/CSOgroup/CALDER2
BugReports: https://github.com/CSOgroup/CALDER2/issues
License: MIT
Encoding: UTF-8
Depends:
    R (>= 3.5.2)
biocViews:
Imports: 
	R.utils (>= 2.9.0),
	doParallel (>= 1.0.15),
	ape (>= 5.3),
	dendextend (>= 1.12.0),
	fitdistrplus (>= 1.0.14),
	igraph (>= 1.2.4),
	Matrix (>= 1.2.17),
	rARPACK (>= 0.11.0),
	factoextra (>= 1.0.5),
	maptools (>= 0.9.5),
	data.table (>= 1.12.2),
	fields (>= 9.8.3),
	GenomicRanges (>= 1.36.0),
	strawr (>= 0.0.9),
	rhdf5 (>= 2.28.0),
	ggplot2 (>= 3.3.5),
	optparse
RoxygenNote: 7.1.2
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
