ArticleBioinformatics (Oxford, England)2018
HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.Nature communications · 2026Article
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Using paired-end read orientations to assess technical biases in capture Hi-C.NAR genomics and bioinformatics · 2024Article
- An endothelial regulatory module links blood pressure regulation with elite athletic performance.PLoS genetics · 2024Article
- Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.Life science alliance · 2024Article
- Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.Nature protocols · 2022Review
- Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Nature protocols · 2021Article
- 3D reconstruction of genomic regions from sparse interaction data.NAR genomics and bioinformatics · 2021Article
- Genetics in Atopic Dermatitis: Historical Perspective and Future Prospects.Acta dermato-venereologica · 2020Review
- A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.Omics : a journal of integrative biology · 2020Article
- CaptureProbe: a java tool for designing probes for capture Hi-C applications.Zoological research · 2020Article
- ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.Genome biology · 2019Article
- High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways.Circulation. Genomic and precision medicine · 2019Article
- Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.Scientific reports · 2019Article
- GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution.BMC genomics · 2019Article
- Whole-genome analysis of haemophilus influenzae invasive strains isolated from Campinas state University hospital. An epidemiological approach 2012 - 2019 and ancestor strains.The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious DiseasesArticle
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications. Availability: https://github.com/sahlenlab/HiCapTools. Contact: pelinak@kth.se. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
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 Socratic graph.