The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
Open accessAbstract
The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.
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Citations
Cites
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
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
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2016.07.002 · Cited by 3,836
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C.-J., Vert, J.-P., Heard, E., Dekker, J., & Barillot, E. (2015) · Genome Biology · doi:10.1186/s13059-015-0831-x · Cited by 2,565 · cited 3×
“Among the above tools, HiC-Pro is the only one with the ability to analyse cHiC and HiChIP data. scHiCNorm (25) and scHiCluster(26) provide support for single-cell Hi-C data normalization and clustering, but suffer from the lack of a tool suite to guide researchers through the workflow of processing single-cell HiC da…”
MethodHiGlass: web-based visual exploration and analysis of genome interaction maps
Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S. B., Azhir, A., Kumar, N., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1486-1 · Cited by 2,453
Cited by
Gu, Z. (2022) · iMeta · doi:10.1002/imt2.43 · Cited by 1,885
Cooltools: Enabling high-resolution Hi-C analysis in Python
Open2C, Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, I. M., Galitsyna, A. A., Goloborodko, A., Imakaev, M., Oksuz, B. A., Venev, S. V., et al. (2024) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012067 · Cited by 313
A compendium of genetic regulatory effects across pig tissues
Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., The PigGTEx Consortium, Bai, L., Cai, Z., Zhao, B., et al. (2024) · Nature Genetics · doi:10.1038/s41588-023-01585-7 · Cited by 266
Kruse, K., Hug, C. B., & Vaquerizas, J. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02215-9 · Cited by 253
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes
Waters, P. D., Patel, H. R., Ruiz-Herrera, A., Álvarez-González, L., Lister, N. C., Simakov, O., Ezaz, T., Kaur, P., Frere, C., Grützner, F., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2112494118 · Cited by 153
Metadata
- Authors
- Wolff, J., Rabbani, L., Gilsbach, R., Richard, G., Manke, T., Backofen, R., & Grüning, B. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-04-17
- Volume
- 48
- Issue
- W1
- Pages
- W177-W184
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3017323102
- Cited by
- 441
- References
- 40
- FWCI
- 11.13
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. https://app.cochat.ai/papers/10.1093/nar/gkaa220
- The paper
- Wolff, J., Rabbani, L., Gilsbach, R., Richard, G., Manke, T., Backofen, R., & Grüning, B. A. (2020). Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa220
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