Package: TopDom 0.10.1

TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

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.

Authors:Henrik Bengtsson [aut, cre, cph], Hanjun Shin [aut, ctr, cph], Harris Lazaris [ctr, cph], Gangqing Hu [ctr, cph], Xianghong Zhou [ctr]

TopDom_0.10.1.tar.gz
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TopDom.pdf |TopDom.html✨
TopDom/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/henrikbengtsson/topdom/issues

On CRAN:

genomicshictopological-domains

9 exports 18 stars 4.33 score 34 dependencies 1 dependents 31 mentions 18 scripts 188 downloads

Last updated 3 years agofrom:5d10e286dd (on master). Checks:OK: 3 NOTE: 4. Indexed: yes.

Exports:countsPerRegionggCountHeatmapggDomainggDomainLabellegacyoverlapScoresreadHiCsubsetByRegionTopDom

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr