We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.
- Authors
Cairns, Jonathan; Orchard, William R; Malysheva, Valeriya; Spivakov, Mikhail
- Abstract
Summary Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package for robust detection of differential interactions in Capture Hi-C data. Chicdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalization and multiple testing procedures that account for specific statistical properties of Capture Hi-C. We validate Chicdiff on published Promoter Capture Hi-C data in human Monocytes and CD4+ T cells, identifying multitudes of cell type-specific interactions, and confirming the overall positive association between promoter interactions and gene expression. Availability and implementation Chicdiff is implemented as an R package that is publicly available at https://github.com/RegulatoryGenomicsGroup/chicdiff. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
KARYOTYPES; PIPELINES; T cells; MONOCYTES; GENE expression
- Publication
Bioinformatics, 2019, Vol 35, Issue 22, p4764
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz450