The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Pathview: an R/Bioconductor package for pathway-based data integration and visualization
Open accessAbstract
Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. Contact: luo_weijun@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.
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KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,172
Reactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Khatri, P., Sirota, M., & Butte, A. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002375 · Cited by 1,566
GAGE: generally applicable gene set enrichment for pathway analysis
Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., & Woolf, P. J. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-161 · Cited by 1,333
Self-citationAnalysing biological pathways in genome-wide association studies
Wang, K., Li, M., & Hakonarson, H. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2884 · Cited by 766
MetPA: a web-based metabolomics tool for pathway analysis and visualization
Xia, J., & Wishart, D. S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq418 · Cited by 766
Graphviz— Open Source Graph Drawing Tools
Ellson, J., Gansner, E., Koutsofios, L., North, S. C., & Woodhull, G. (2002) · Lecture Notes in Computer Science · doi:10.1007/3-540-45848-4_57 · Cited by 761
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Zhang, J. D., & Wiemann, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp167 · Cited by 331
Pathway analysis of kidney cancer using proteomics and metabolic profiling
Perroud, B., Lee, J., Valkova, N., Dhirapong, A., Lin, P.-Y., Fiehn, O., Kültz, D., & Weiss, R. H. (2006) · Molecular Cancer · doi:10.1186/1476-4598-5-64 · Cited by 233
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Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss
Arun, G., Diermeier, S., Akerman, M., Chang, K.-C., Wilkinson, J. E., Hearn, S., Kim, Y., MacLeod, A. R., Krainer, A. R., Norton, L., et al. (2016) · Genes & Development · doi:10.1101/gad.270959.115 · Cited by 585
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Westermann, A. J., Förstner, K. U., Amman, F., Barquist, L., Chao, Y., Schulte, L. N., Müller, L., Reinhardt, R., Stadler, P. F., & Vogel, J. (2016) · Nature · doi:10.1038/nature16547 · Cited by 499
Ulgen, E., Ozisik, O., & Sezerman, O. U. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00858 · Cited by 469
Pathview Web: user friendly pathway visualization and data integration
Luo, W., Pant, G., Bhavnasi, Y. K., Blanchard, S. G., & Brouwer, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx372 · Cited by 438
Self-citationArthur, J. C., Gharaibeh, R. Z., Mühlbauer, M., Perez-Chanona, E., Uronis, J. M., McCafferty, J., Fodor, A. A., & Jobin, C. (2014) · Nature Communications · doi:10.1038/ncomms5724 · Cited by 392
Metadata
- Authors
- Luo, W., & Brouwer, C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-06-04
- Volume
- 29
- Issue
- 14
- Pages
- 1830-1831
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2141224543
- Cited by
- 2,284
- References
- 12
- FWCI
- 19.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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