ArticleBioinformatics (Oxford, England)2020
Coolpup.py: versatile pile-up analysis of Hi-C data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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146 citing papers in PubMed.
- Spatially resolved chromatin architectures in mammalian brain tissues.Nature methods · 2026Article
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- Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain.Nature communications · 2026Article
- High-resolution chromatin mapping reveals that CTCF anchors meiotic loops to the chromosome axis.Nature communications · 2026Article
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- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species.Nature methods · 2026Article
- Replication-independent eviction of the histone variant H2B.8 reveals chromatin reprogramming during seed imbibition.Nature communications · 2026Article
- XPF-like domain in human SHOC1 is required for crossover formation and protecting autosome from MSUC.Nucleic acids research · 2026Article
- H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs.Nature genetics · 2026Article
- An Adnp frameshift variant disrupts Wnt signalling inducing chromatocytoskeletal defects and autism-related behaviour in male mice.EBioMedicine · 2026Article
- Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.Molecular cell · 2026Article
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- Cooperative Roles of Pds5a and Pds5b Constrain Long-Range Chromatin Interactions in Vertebrate Embryos.Development, growth & differentiation · 2026Article
- Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.Nature neuroscience · 2026Article
- Z-DNA formation regulates the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization.Nature structural & molecular biology · 2026Article
- Stage-specific epigenetic priming amplifies gene activation during lineage commitment.Science advances · 2026Article
86 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
motivationHi-C is currently the method of choice to investigate the global 3D organization of the genome. A major limitation of Hi-C is the sequencing depth required to robustly detect loops in the data. A popular approach used to mitigate this issue, even in single-cell Hi-C data, is genome-wide averaging (piling-up) of peaks, or other features, annotated in high-resolution datasets, to measure their prominence in less deeply sequenced data. However, current tools do not provide a computationally efficient and versatile implementation of this approach.
resultsHere, we describe coolpup.py-a versatile tool to perform pile-up analysis on Hi-C data. We demonstrate its utility by replicating previously published findings regarding the role of cohesin and CTCF in 3D genome organization, as well as discovering novel details of Polycomb-driven interactions. We also present a novel variation of the pile-up approach that can aid the statistical analysis of looping interactions. We anticipate that coolpup.py will aid in Hi-C data analysis by allowing easy to use, versatile and efficient generation of pile-ups. AVAILABILITY AND IMPLEMENTATION: Coolpup.py is cross-platform, open-source and free (MIT licensed) software. Source code is available from https://github.com/Phlya/coolpuppy and it can be installed from the Python Packaging Index.
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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.