The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
Open accessAbstract
Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. Availability and Implementation: The web-interface is accessible via http://cgenome.net/calypso/. The software is programmed in Java, PERL and R and the source code is available from Zenodo (https://zenodo.org/record/50931). The software is freely available for non-commercial users. Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,322
STAMP: statistical analysis of taxonomic and functional profiles
Parks, D. H., Tyson, G. W., Hugenholtz, P., & Beiko, R. G. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu494 · Cited by 4,191
Differential abundance analysis for microbial marker-gene surveys
Paulson, J. N., Stine, O. C., Bravo, H. C., & Pop, M. (2013) · Nature Methods · doi:10.1038/nmeth.2658 · Cited by 2,428
The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
D Ainsworth, T., Krause, L., Bridge, T., Torda, G., Raina, J.-B., Zakrzewski, M., Gates, R. D., Padilla-Gamiño, J. L., Spalding, H. L., Smith, C., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.39 · Cited by 549
Self-citationMETAGENassist: a comprehensive web server for comparative metagenomics
Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A. C., Cruz, J. A., Sinelnikov, I., Budwill, K., Nesbo, C. L., & Wishart, D. S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks497 · Cited by 408
Impact of Experimental Hookworm Infection on the Human Gut Microbiota
Cantacessi, C., Giacomin, P., Croese, J., Zakrzewski, M., Sotillo, J., McCann, L., Nolan, M. J., Mitreva, M., Krause, L., & Loukas, A. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiu256 · Cited by 165
Self-citationShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Kristiansson, E., Hugenholtz, P., & Dalevi, D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp508 · Cited by 138
Swe, P. M., Zakrzewski, M., Kelly, A., Krause, L., & Fischer, K. (2014) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0002897 · Cited by 88
Self-citationFANTOM: Functional and taxonomic analysis of metagenomes
Sanli, K., Karlsson, F. H., Nookaew, I., & Nielsen, J. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-38 · Cited by 37
Cited by
Current challenges and best-practice protocols for microbiome analysis
Bharti, R., & Grimm, D. G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbz155 · Cited by 592
Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus
Wang, J., Zheng, J., Shi, W., Du, N., Xu, X., Zhang, Y., Ji, P., Zhang, F., Jia, Z., Wang, Y., et al. (2018) · Gut · doi:10.1136/gutjnl-2018-315988 · Cited by 452
Perinatal factors affect the gut microbiota up to four years after birth
Fouhy, F., Watkins, C., Hill, C. J., O’Shea, C.-A., Nagle, B., Dempsey, E. M., O’Toole, P. W., Ross, R. P., Ryan, C. A., & Stanton, C. (2019) · Nature Communications · doi:10.1038/s41467-019-09252-4 · Cited by 274
Mörkl, S., Lackner, S., Müller, W., Gorkiewicz, G., Kashofer, K., Oberascher, A., Painold, A., Holl, A., Holzer, P., Meinitzer, A., et al. (2017) · International Journal of Eating Disorders · doi:10.1002/eat.22801 · Cited by 181
Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study
Stadlbauer, V., Engertsberger, L., Komarova, I., Feldbacher, N., Leber, B., Pichler, G., Fink, N., Scarpatetti, M., Schippinger, W., Schmidt, R., et al. (2020) · BMC Geriatrics · doi:10.1186/s12877-020-01644-2 · Cited by 182
Metadata
- Authors
- Zakrzewski, M., Proietti, C., Ellis, J. J., Hasan, S., Brion, M.-J., Berger, B., & Krause, L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-12-13
- Volume
- 33
- Issue
- 5
- Pages
- 782-783
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2346423776
- Cited by
- 567
- References
- 9
- FWCI
- 25.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions. https://app.cochat.ai/papers/10.1093/bioinformatics/btw725
- The paper
- Zakrzewski, M., Proietti, C., Ellis, J. J., Hasan, S., Brion, M.-J., Berger, B., & Krause, L. (2017). Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions. Bioinformatics. https://doi.org/10.1093/bioinformatics/btw725
Data sources
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.
