The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Open accessAbstract
BACKGROUND: Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. RESULTS: Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. CONCLUSIONS: On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.
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Cites
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
An improved Bonferroni procedure for multiple tests of significance
SIMES, R. J. (1986) · Biometrika · doi:10.1093/biomet/73.3.751 · Cited by 2,396
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · cited 1×
“Future development of diffHic will aim to accommodate other types of chromatin conformation data, such as DNase Hi-C [34] and Capture-C [35].”
BackgroundCohesin-mediated interactions organize chromosomal domain architecture
Sofueva, S., Yaffe, E., Chan, W., Georgopoulou, D., Vietri Rudan, M., Mira‐Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., & Hadjur, S. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.237 · Cited by 394
The Spatial Organization of the Human Genome
Bickmore, W. A. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153515 · Cited by 391
Lin, Y. C., Benner, C., Mansson, R., Heinz, S., Miyazaki, K., Miyazaki, M., Chandra, V., Bossen, C., Glass, C. K., & Murre, C. (2012) · Nature Immunology · doi:10.1038/ni.2432 · Cited by 281
Cited by
Chen, Y., Lun, A. T. L., & Smyth, G. K. (2016) · F1000Research · doi:10.12688/f1000research.8987.1 · Cited by 1,287
Self-citationChen, Y., Chen, L., Lun, A. T. L., Baldoni, P. L., & Smyth, G. K. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf018 · Cited by 816
Self-citationGenome-wide mapping and analysis of chromosome architecture
Schmitt, A. D., Hu, M., & Ren, B. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.104 · Cited by 344
Comparison of computational methods for Hi-C data analysis
Forcato, M., Nicoletti, C., Pal, K., Livi, C. M., Ferrari, F., & Bicciato, S. (2017) · Nature Methods · doi:10.1038/nmeth.4325 · Cited by 312
Kruse, K., Hug, C. B., & Vaquerizas, J. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02215-9 · Cited by 253
Metadata
- Authors
- Lun, A. T. L., & Smyth, G. K.
- Venue
- BMC Bioinformatics
- Published
- 2015-08-19
- Volume
- 16
- Issue
- 1
- Pages
- 258-258
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1862913282
- Cited by
- 211
- References
- 9
- FWCI
- 5.15
- Type
- journal article
- Language
- en
- Open access
- gold
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- Lun, A. T. L., & Smyth, G. K. (2015). diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics. https://doi.org/10.1186/s12859-015-0683-0
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