The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
Abstract
Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA).
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Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259
Self-citationMolecular mechanisms of epithelial–mesenchymal transition
Lamouille, S., Xu, J., & Derynck, R. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3758 · Cited by 8,091
GREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
The human transcriptome across tissues and individuals
Melé, M., Ferreira, P. G., Reverter, F., DeLuca, D. S., Monlong, J., Sammeth, M., Young, T. R., Goldmann, J. M., Pervouchine, D. D., Sullivan, T. J., et al. (2015) · Science · doi:10.1126/science.aaa0355 · Cited by 1,304
Widespread plasticity in CTCF occupancy linked to DNA methylation
Wang, H., Maurano, M. T., Qu, H., Varley, K. E., Gertz, J., Pauli, F., Lee, K., Canfield, T., Weaver, M., Sandstrom, R., et al. (2012) · Genome Research · doi:10.1101/gr.136101.111 · Cited by 588
Pemberton, H., Anderton, E., Patel, H., Brookes, S., Chandler, H., Palermo, R., Stock, J., Rodriguez-Niedenführ, M., Racek, T., de Breed, L., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r23 · Cited by 50
Cited by
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
(2021) · doi:10.1016/j.xinn.2021.100141 · Cited by 12,455
A human liver cell atlas reveals heterogeneity and epithelial progenitors
Aizarani, N., Saviano, A., Sagar, Mailly, L., Durand, S., Herman, J. S., Pessaux, P., Baumert, T. F., & Grün, D. (2019) · Nature · doi:10.1038/s41586-019-1373-2 · Cited by 1,147
Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.037 · Cited by 1,046
Multi-omic machine learning predictor of breast cancer therapy response
Sammut, S.-J., Crispin-Ortuzar, M., Chin, S.-F., Provenzano, E., Bardwell, H. A., Ma, W., Cope, W., Dariush, A., Dawson, S.-J., Abraham, J. E., et al. (2022) · Nature · doi:10.1038/s41586-021-04278-5 · Cited by 654
Deep Visual Proteomics defines single-cell identity and heterogeneity
Mund, A., Coscia, F., Kriston, A., Hollandi, R., Kovács, F., Brunner, A.-D., Migh, E., Schweizer, L., Santos, A., Bzorek, M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01302-5 · Cited by 562
Metadata
- Authors
- Yu, G., & He, Q.-Y.
- Venue
- Molecular BioSystems
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-23
- Volume
- 12
- Issue
- 2
- Pages
- 477-479
- ISSN
- 1742-2051 (ISSN-L)
- 1742-206X
- OpenAlex
- W2172557341
- Cited by
- 1,918
- References
- 7
- FWCI
- 14.54
- Type
- journal article
- Language
- en
- Open access
- closed
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- Yu, G., & He, Q.-Y. (2015). ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. https://doi.org/10.1039/c5mb00663e
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
