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

13 NOTE

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	99.5s
r-devel-linux-x86_64-debian-gcc	NOTE	68.2s
r-devel-linux-x86_64-fedora-clang	NOTE	165.3s
r-devel-linux-x86_64-fedora-gcc	NOTE	146.9s
r-devel-windows-x86_64	NOTE	110s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	71s
r-oldrel-windows-x86_64	NOTE	145s
r-patched-linux-x86_64	NOTE	90.5s
r-release-linux-x86_64	NOTE
r-release-macos-arm64	NOTE	25s
r-release-macos-x86_64	NOTE	133s
r-release-windows-x86_64	NOTE	110s

Check details (15 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-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 10, 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

1 tracked

new 0.10.1 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN May 6, 2021. Releases before tracking aren’t shown.