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:
TopDom_0.10.1.tar.gz
TopDom_0.10.1.zip(r-4.5)TopDom_0.10.1.zip(r-4.4)TopDom_0.10.1.zip(r-4.3)
TopDom_0.10.1.tgz(r-4.4-any)TopDom_0.10.1.tgz(r-4.3-any)
TopDom_0.10.1.tar.gz(r-4.5-noble)TopDom_0.10.1.tar.gz(r-4.4-noble)
TopDom_0.10.1.tgz(r-4.4-emscripten)TopDom_0.10.1.tgz(r-4.3-emscripten)
TopDom.pdf |TopDom.html✨
TopDom/json (API)
NEWS
| # Install 'TopDom' in R: |
| install.packages('TopDom', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/henrikbengtsson/topdom/issues
genomicshictopological-domains
Last updated 4 years agofrom:5d10e286dd (on master). Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win | NOTE | Nov 14 2024 |
| R-4.5-linux | NOTE | Nov 14 2024 |
| R-4.4-win | NOTE | Nov 14 2024 |
| R-4.4-mac | NOTE | Nov 14 2024 |
| R-4.3-win | OK | Nov 14 2024 |
| R-4.3-mac | OK | Nov 14 2024 |
Exports:countsPerRegionggCountHeatmapggDomainggDomainLabellegacyoverlapScoresreadHiCsubsetByRegionTopDom
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculates Counts per Region in a TopDomData Object | countsPerRegion |
| Produce a Count Heatmap | ggCountHeatmap |
| Add a Topological Domain to a Count Heatmap | ggDomain |
| Add a Topological Domain Label to a Count Heatmap | ggDomainLabel |
| Easy Access to the Original TopDom 0.0.1 and 0.0.2 Implementations | legacy |
| Calculates Overlap Scores Between Two Sets of Topological Domains | overlapScores |
| Reads Hi-C Contact Data from File | readHiC |
| Subset a TopDomData Object by Region | subsetByRegion |
| Identify Topological Domains from a Hi-C Contact Matrix | TopDom |
| Data for the TopDom Package | TopDom-data |
