Distributed under Creative Commons Cc-by 4.0 Rhea: a Transparent and Modular R Pipeline for Microbial Profiling Based on 16s Rrna Gene Amplicons
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Sandra Fischer | Thomas Clavel | I. Lagkouvardos | T. Clavel | Ilias Lagkouvardos | Neeraj Kumar | Neeraj Kumar | Sandra Fischer | Blanca B Landa
[1] I. Martínez,et al. Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species , 2013, PloS one.
[2] Peter R. Minchin,et al. An evaluation of the relative robustness of techniques for ecological ordination , 1987 .
[3] H. Daniel,et al. Gut barrier impairment by high-fat diet in mice depends on housing conditions. , 2016, Molecular nutrition & food research.
[4] Marti J. Anderson,et al. A new method for non-parametric multivariate analysis of variance in ecology , 2001 .
[5] D. Haller,et al. Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men. , 2015, Molecular nutrition & food research.
[6] Susan P. Holmes,et al. Waste Not , Want Not : Why Rarefying Microbiome Data is Inadmissible . October 1 , 2013 , 2013 .
[7] U. Kulozik,et al. Physiological relevance of food grade microcapsules: Impact of milk protein based microcapsules on inflammation in mouse models for inflammatory bowel diseases. , 2015, Molecular nutrition & food research.
[8] L. Jost. Partitioning diversity into independent alpha and beta components. , 2007, Ecology.
[9] Karoline Faust,et al. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. , 2016, FEMS microbiology reviews.
[10] K. Pearson,et al. DETERMINATION OF THE COEFFICIENT OF CORRELATION. , 1909, Science.
[11] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[12] W. Bossert,et al. The Measurement of Diversity , 2001 .
[13] Robert C. Edgar,et al. UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.
[14] M. Horn,et al. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies , 2016, Scientific Reports.
[15] Fionn Murtagh,et al. Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion? , 2011, Journal of Classification.
[16] Susan Holmes,et al. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.
[17] C. Huttenhower,et al. The microbiome quality control project: baseline study design and future directions , 2015, Genome Biology.
[18] R. Gentleman,et al. Independent filtering increases detection power for high-throughput experiments , 2010, Proceedings of the National Academy of Sciences.
[19] Martin Hartmann,et al. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.
[20] Piotr Gawron,et al. VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data , 2015, Microbiome.
[21] Philip H. Ramsey. Nonparametric Statistical Methods , 1974, Technometrics.
[22] L. Jost. Entropy and diversity , 2006 .
[23] Sang Joon Kim,et al. A Mathematical Theory of Communication , 2006 .
[24] A. Hiergeist,et al. Microbiome sequencing: challenges and opportunities for molecular medicine , 2016, Expert review of molecular diagnostics.
[25] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[26] R. Knight,et al. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities , 2007, Applied and Environmental Microbiology.
[27] Brian C. Thomas,et al. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants , 2014, Microbiome.
[28] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[29] J. T. Curtis,et al. An Ordination of the Upland Forest Communities of Southern Wisconsin , 1957 .
[30] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[31] Scot E. Dowd,et al. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples , 2016, Gut Pathogens.
[32] John Aitchison,et al. The Statistical Analysis of Compositional Data , 1986 .
[33] M. Kendall. Statistical Methods for Research Workers , 1937, Nature.
[34] Hongzhe Li,et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances , 2012, Bioinform..
[35] Susan P. Holmes,et al. Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking , 2014, Bioinform..
[36] Christopher J Cates,et al. Simpson's paradox and calculation of number needed to treat from meta-analysis , 2002, BMC medical research methodology.
[37] B. Tjaden,et al. De novo assembly of bacterial transcriptomes from RNA-seq data , 2015, Genome Biology.
[38] Jawed Alam,et al. Helicobacter pylori strains harboring babA2 from Indian sub population are associated with increased virulence in ex vivo study , 2016, Gut Pathogens.
[39] A. Gessner,et al. Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. , 2016, International journal of medical microbiology : IJMM.
[40] Falk Hildebrand,et al. Erratum to: LotuS: an efficient and user-friendly OTU processing pipeline , 2014, Microbiome.
[41] Karen P. Scott,et al. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice , 2015, Microbiome.
[42] Martin von Bergen,et al. Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence , 2015, Gut.
[43] Peter R. Minchin,et al. An evaluation of the relative robustness of techniques for ecological ordination , 1987, Vegetatio.
[44] R. Feise. Do multiple outcome measures require p-value adjustment? , 2002, BMC medical research methodology.