The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
Open accessAbstract
Summary: Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize and transform results from various classifiers—such as Kraken, Centrifuge and MethaPhlAn—using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection. Availability and implementation: Pavian is implemented in the R language as a modular Shiny web app and is freely available under GPL-3 from http://github.com/fbreitwieser/pavian.
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Cites
Kraken: ultrafast metagenomic sequence classification using exact alignments
Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521
Self-citationReagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185
Centrifuge: rapid and sensitive classification of metagenomic sequences
Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016) · Genome Research · doi:10.1101/gr.210641.116 · Cited by 1,438
Self-citationActionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
Wilson, M. R., Naccache, S. N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S. M., Somasekar, S., Federman, S., Miller, S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1401268 · Cited by 977
Research works printed but not linked: 6
- Bostock, 2011, D³ data-driven documents, IEEE Trans. Vis. Comput. Graph, 17, 2301, 10.1109/TVCG.2011.185 · DOI · Paper page
- Breitwieser, 2018, KrakenUniq: confident and fast metagenomics classification using unique k-mer counts, Genome Biol, 19, 198, 10.1186/s13059-018-1568-0 · DOI · Paper page
- Breitwieser, 2017, A review of methods and databases for metagenomic classification and assembly, Brief. Bioinform
- McMurdie, 2015, Shiny-phyloseq: web application for interactive microbiome analysis with provenance tracking, Bioinformatics, 31, 282, 10.1093/bioinformatics/btu616 · DOI · Paper page
- Salzberg, 2016, Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system, Neurol. Neuroimmunol. Neuroinflamm, 3, e251, 10.1212/NXI.0000000000000251 · doi:10.1212/nxi.0000000000000251
- Wagner, 2018, Metaviz: interactive statistical and visual analysis of metagenomic data, Nucleic Acids Res, 46, 2777, 10.1093/nar/gky136 · DOI
Cited by
Simner, P. J., Miller, S., & Carroll, K. C. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/cix881 · Cited by 821
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
Breitwieser, F. P., Baker, D. N., & Salzberg, S. L. (2018) · Genome Biology · doi:10.1186/s13059-018-1568-0 · Cited by 474
Self-citationClustering predicted structures at the scale of the known protein universe
Barrio-Hernandez, I., Yeo, J., Jänes, J., Mirdita, M., Gilchrist, C. L. M., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature · doi:10.1038/s41586-023-06510-w · Cited by 362
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age
Lieberman, N. A. P., Peddu, V., Xie, H., Shrestha, L., Huang, M.-L., Mears, M. C., Cajimat, M. N., Bente, D. A., Shi, P.-Y., Bovier, F., et al. (2020) · PLOS Biology · doi:10.1371/journal.pbio.3000849 · Cited by 267
Steinegger, M., & Salzberg, S. L. (2020) · Genome Biology · doi:10.1186/s13059-020-02023-1 · Cited by 246
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Metadata
- Authors
- Breitwieser, F. P., & Salzberg, S. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-09-25
- Volume
- 36
- Issue
- 4
- Pages
- 1303-1304
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2977180444
- Cited by
- 483
- References
- 5
- FWCI
- 10.38
- Type
- journal article
- Language
- en
- Open access
- bronze
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Funders
- National Institutes of Health (R35-GM130151, R01-HG006677)
- U. S. Army Research Office (W911NF-14-1-0490)
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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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