TopDom

An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

v0.10.1 · May 6, 2021 · GPL

Description

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.

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CRAN Check Status

14 NOTE

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	97.3s
r-devel-linux-x86_64-debian-gcc	NOTE	67.7s
r-devel-linux-x86_64-fedora-clang	NOTE	150.8s
r-devel-linux-x86_64-fedora-gcc	NOTE	144.6s
r-devel-macos-arm64	NOTE	24s
r-devel-windows-x86_64	NOTE	107s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	57s
r-oldrel-windows-x86_64	NOTE	134s
r-patched-linux-x86_64	NOTE	90.6s
r-release-linux-x86_64	NOTE	90.2s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	71s
r-release-windows-x86_64	NOTE	106s

Check details (16 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Henrik Bengtsson <henrikb@braju.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^

Reverse Dependencies (1)

imports

rnaCrosslinkOO

Dependency Network

Version History

new 0.10.1 Mar 9, 2026

Maintainer

Henrik Bengtsson

Dependencies

Depends

R (>= 3.3.0)

Imports

matrixStats grid ggplot2 reshape2 tibble

Suggests

diffobj (>= 0.1.11)

Compilation

No compilation needed

First Published

Mar 9, 2026

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