The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.
diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Open accessAbstract
ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification "hotspots". diffReps is developed in PERL programming language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.
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Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3
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Self-citationFrom reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Yan, F., Powell, D. R., Curtis, D. J., & Wong, N. C. (2020) · Genome Biology · doi:10.1186/s13059-020-1929-3 · Cited by 473
FTO mediates LINE1 m 6 A demethylation and chromatin regulation in mESCs and mouse development
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Self-citationA Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis
Berg, D. A., Su, Y., Jimenez-Cyrus, D., Patel, A., Huang, N., Morizet, D., Lee, S., Shah, R., Ringeling, F. R., Jain, R., et al. (2019) · Cell · doi:10.1016/j.cell.2019.02.010 · Cited by 267
Metadata
- Authors
- Shen, L., Shao, N.-Y., Liu, X., Maze, I., Feng, J., & Nestler, E. J.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-06-10
- Volume
- 8
- Issue
- 6
- Pages
- e65598
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2085184586
- Cited by
- 403
- References
- 33
- FWCI
- 7.26
- Type
- journal article
- Language
- en
- Open access
- gold
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- Shen, L., Shao, N.-Y., Liu, X., Maze, I., Feng, J., & Nestler, E. J. (2013). diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates. PLoS ONE. https://doi.org/10.1371/journal.pone.0065598
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