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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.
| Version: | 0.10.1 |
| Depends: | R (≥ 3.3.0) |
| Imports: | matrixStats, grid, ggplot2, reshape2, tibble |
| Suggests: | diffobj (≥ 0.1.11) |
| Published: | 2021-05-06 |
| DOI: | 10.32614/CRAN.package.TopDom |
| Author: | 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] |
| Maintainer: | Henrik Bengtsson <henrikb at braju.com> |
| BugReports: | https://github.com/HenrikBengtsson/TopDom/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL] |
| URL: | https://github.com/HenrikBengtsson/TopDom |
| NeedsCompilation: | no |
| Citation: | TopDom citation info |
| Materials: | README NEWS |
| CRAN checks: | TopDom results |
| Reference manual: | TopDom.pdf |
| Package source: | TopDom_0.10.1.tar.gz |
| Windows binaries: | r-devel: TopDom_0.10.1.zip, r-release: TopDom_0.10.1.zip, r-oldrel: TopDom_0.10.1.zip |
| macOS binaries: | r-release (arm64): TopDom_0.10.1.tgz, r-oldrel (arm64): TopDom_0.10.1.tgz, r-release (x86_64): TopDom_0.10.1.tgz, r-oldrel (x86_64): TopDom_0.10.1.tgz |
| Reverse imports: | rnaCrosslinkOO |
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These binaries (installable software) and packages are in development.
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