Coolsecture: an easy-to-use and improved framework for cross-species Hi-C contact map comparison.

Peng-Kai Zhu, Jiang-Qi Pan, Zhan-Chao Cheng, Jian Gao

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Peng-Kai ZhuKey Laboratory of National Forestry and Grassland Administration on Bamboo & Rattan, International Center for Bamboo and Rattan, Beijing 100102, China.ORCID 0009-0007-5598-1300

Jiang-Qi PanCenter for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.

Zhan-Chao ChengKey Laboratory of National Forestry and Grassland Administration on Bamboo & Rattan, International Center for Bamboo and Rattan, Beijing 100102, China.

Jian GaoKey Laboratory of National Forestry and Grassland Administration on Bamboo & Rattan, International Center for Bamboo and Rattan, Beijing 100102, China.

Funding

National Key Research and Development Program of China 2021YFD2200505National Natural Science Foundation of China 32071849

6 · The paper itself

Abstract

summaryCross-species Hi-C comparison remains challenging because existing workflows often rely on multiple scripts, heterogeneous I/O formats, and limited diagnostic support. We present coolsecture, a Python 3 command-line toolkit that integrates multiple contact-matrix and synteny formats with bidirectional lift-over and reciprocal consistency assessment, multi-resolution percentile-based comparison, diagnostic visualization, and cross-sample similarity analysis, providing a streamlined and reproducible framework for comparative Hi-C analysis. AVAILABILITY AND IMPLEMENTATION: coolsecture is distributed under the GPL-3 license. Source code, Snakemake workflows, and documentation are freely available at https://github.com/pk-zhu/Coolsecture and are archived on Figshare at https://doi.org/10.6084/m9.figshare.30158440.

Indexed as

SoftwareAnimals

Identifiers

PMID42752541

DOI10.1093/bioinformatics/btag683

PMCPMC13633847

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.