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ENH: added citations #196
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Original file line number | Diff line number | Diff line change |
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@article{lozupone2005unifrac, | ||
title={UniFrac: a new phylogenetic method for comparing microbial communities}, | ||
author={Lozupone, Catherine and Knight, Rob}, | ||
journal={Applied and environmental microbiology}, | ||
volume={71}, | ||
number={12}, | ||
pages={8228--8235}, | ||
year={2005}, | ||
publisher={Am Soc Microbiol}, | ||
doi={10.1128/AEM.71.12.8228-8235.2005} | ||
} | ||
|
||
@article{lozupone2007quantitative, | ||
title={Quantitative and qualitative $\beta$ diversity measures lead to different insights into factors that structure microbial communities}, | ||
author={Lozupone, Catherine A and Hamady, Micah and Kelley, Scott T and Knight, Rob}, | ||
journal={Applied and environmental microbiology}, | ||
volume={73}, | ||
number={5}, | ||
pages={1576--1585}, | ||
year={2007}, | ||
publisher={Am Soc Microbiol}, | ||
doi={10.1128/AEM.01996-06} | ||
} | ||
|
||
@article{chang2011variance, | ||
title={Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny}, | ||
author={Chang, Qin and Luan, Yihui and Sun, Fengzhu}, | ||
journal={BMC bioinformatics}, | ||
volume={12}, | ||
number={1}, | ||
pages={118}, | ||
year={2011}, | ||
publisher={BioMed Central}, | ||
doi={https://doi.org/10.1186/1471-2105-12-118} | ||
} | ||
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@article{chen2012associating, | ||
title={Associating microbiome composition with environmental covariates using generalized UniFrac distances}, | ||
author={Chen, Jun and Bittinger, Kyle and Charlson, Emily S and Hoffmann, Christian and Lewis, James and Wu, Gary D and Collman, Ronald G and Bushman, Frederic D and Li, Hongzhe}, | ||
journal={Bioinformatics}, | ||
volume={28}, | ||
number={16}, | ||
pages={2106--2113}, | ||
year={2012}, | ||
publisher={Oxford University Press}, | ||
doi={10.1093/bioinformatics/bts342} | ||
} | ||
|
||
@article{faith1992conservation, | ||
title={Conservation evaluation and phylogenetic diversity}, | ||
author={Faith, Daniel P}, | ||
journal={Biological conservation}, | ||
volume={61}, | ||
number={1}, | ||
pages={1--10}, | ||
year={1992}, | ||
publisher={Elsevier}, | ||
doi={https://doi.org/10.1016/0006-3207(92)91201-3} | ||
} | ||
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||
@article{vazquez2013emperor, | ||
title={EMPeror: a tool for visualizing high-throughput microbial community data}, | ||
author={V{\'a}zquez-Baeza, Yoshiki and Pirrung, Meg and Gonzalez, Antonio and Knight, Rob}, | ||
journal={Gigascience}, | ||
volume={2}, | ||
number={1}, | ||
pages={16}, | ||
year={2013}, | ||
publisher={BioMed Central}, | ||
doi={10.1186/2047-217X-2-16} | ||
} | ||
|
||
@article{sorensen1948method, | ||
title={A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons}, | ||
author={S{\o}rensen, Thorvald}, | ||
journal={Biol. Skr.}, | ||
volume={5}, | ||
pages={1--34}, | ||
year={1948} | ||
} | ||
|
||
@article{jaccard1908nouvelles, | ||
title={Nouvelles recherches sur la distribution floral}, | ||
author={Jaccard, P}, | ||
journal={Bull. Soc. Vard. Sci. Nat}, | ||
volume={44}, | ||
pages={223--270}, | ||
year={1908} | ||
} | ||
|
||
@article{pielou1966measurement, | ||
title={The measurement of diversity in different types of biological collections}, | ||
author={Pielou, Evelyn C}, | ||
journal={Journal of theoretical biology}, | ||
volume={13}, | ||
pages={131--144}, | ||
year={1966}, | ||
publisher={Elsevier}, | ||
doi={https://doi.org/10.1016/0022-5193(66)90013-0} | ||
} | ||
|
||
@article{clarke1993method, | ||
title={A method of linking multivariate community structure to environmental variables}, | ||
author={Clarke, KR and Ainsworth, M}, | ||
journal={Marine ecology progress series}, | ||
pages={205--219}, | ||
year={1993}, | ||
publisher={JSTOR} | ||
} | ||
|
||
@article{kruskal1952use, | ||
title={Use of ranks in one-criterion variance analysis}, | ||
author={Kruskal, William H and Wallis, W Allen}, | ||
journal={Journal of the American statistical Association}, | ||
volume={47}, | ||
number={260}, | ||
pages={583--621}, | ||
year={1952}, | ||
publisher={Taylor \& Francis} | ||
} | ||
|
||
@article{anderson2001new, | ||
title={A new method for non-parametric multivariate analysis of variance}, | ||
author={Anderson, Marti J}, | ||
journal={Austral ecology}, | ||
volume={26}, | ||
number={1}, | ||
pages={32--46}, | ||
year={2001}, | ||
publisher={Wiley Online Library}, | ||
doi={https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x} | ||
} | ||
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||
@article{mantel1967detection, | ||
title={The detection of disease clustering and a generalized regression approach}, | ||
author={Mantel, Nathan}, | ||
journal={Cancer research}, | ||
volume={27}, | ||
number={2 Part 1}, | ||
pages={209--220}, | ||
year={1967}, | ||
publisher={AACR} | ||
} | ||
|
||
@article{pearson1895note, | ||
title={Note on regression and inheritance in the case of two parents}, | ||
author={Pearson, Karl}, | ||
journal={Proceedings of the Royal Society of London}, | ||
volume={58}, | ||
pages={240--242}, | ||
year={1895}, | ||
publisher={JSTOR} | ||
} | ||
|
||
@article{spearman1904proof, | ||
title={The proof and measurement of association between two things}, | ||
author={Spearman, Charles}, | ||
journal={The American journal of psychology}, | ||
volume={15}, | ||
number={1}, | ||
pages={72--101}, | ||
year={1904}, | ||
publisher={JSTOR} | ||
} |
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I hate to say this after all your work, but the pipelines won't typically need citations on their own, as the actions they call are tracked in provenance (and so are their citations). Pipelines only need references if their doing something like open-reference.
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oh right of course! No problem — the pipelines are the minority, and I just copied/pasted the other citations so it really didn't add work.