R (>= 1.8.0), MASS, calibrate, HardyWeinberg

An Efficient and Deterministic Method for Identifying
Topological Domains in Genomes
matrixStats, grid, ggplot2, reshape2, tibble
c(person("Henrik", "Bengtsson", role = c("aut", "cre", "cph"),
email = "henrikb@braju.com"),
person("Hanjun", "Shin", role = c("aut", "ctr", "cph"),
email = "shanjun@usc.edu"),
person("Harris", "Lazaris", role = c("ctr", "cph"),
comment = "PhD Student, NYU"),
person("Gangqing", "Hu", role = c("ctr", "cph"),
comment = "Staff Scientist, NIH"),
person("Xianghong", "Zhou", role = c("ctr"),
email = "XJZhou@mednet.ucla.edu"))
The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 <doi:10.1093/nar/gkv1505>).  The authors published an implementation of their method as an R script (two different versions; also available in this package).  This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation.  It also provides a small number of bug fixes to the original code.
Henrik Bengtsson [aut, cre, cph],
Hanjun Shin [aut, ctr, cph],
Harris Lazaris [ctr, cph] (PhD Student, NYU),
Gangqing Hu [ctr, cph] (Staff Scientist, NIH),
Xianghong Zhou [ctr]

Inference, aggregation and visualization for top-k ranked lists
Michael G. Schimek, Medical University of Graz, Graz, Austria; Eva Budinska, Masaryk University, Brno, Czech Republic; Jie Ding, Harvard University, Cambridge, Massachusetts, USA;  Karl G. Kugler, Helmholtz Centre Munich, Neuherberg, Germany; Vendula Svendova, Medical University of Graz, Graz, Austria; Shili Lin, The Ohio State University, Columbus, Ohio, USA.
For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.