phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
暂无分享,去创建一个
[1] A. L. V. D. Wollenberg. Redundancy analysis an alternative for canonical correlation analysis , 1977 .
[2] D. Chessel,et al. From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. , 2004, Journal of theoretical biology.
[3] P. Fayers,et al. The Visual Display of Quantitative Information , 1990 .
[4] Klaus Peter Schliep,et al. phangorn: phylogenetic analysis in R , 2010, Bioinform..
[5] R. Knight,et al. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers , 2008, Nucleic acids research.
[6] Robert Gentleman,et al. Statistical Analyses and Reproducible Research , 2007 .
[7] Philip Hugenholtz,et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes , 2006, Nucleic Acids Res..
[8] Katherine H. Huang,et al. Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.
[9] P. Legendre,et al. vegan : Community Ecology Package. R package version 1.8-5 , 2007 .
[10] Marti J. Anderson,et al. Multivariate dispersion as a measure of beta diversity. , 2006, Ecology letters.
[11] R. Knight,et al. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.
[12] Jun Ma,et al. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences , 2012, BMC Bioinformatics.
[13] Hadley Wickham,et al. Reshaping Data with the reshape Package , 2007 .
[14] Peter R. Minchin,et al. An evaluation of the relative robustness of techniques for ecological ordination , 1987, Vegetatio.
[15] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[16] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[17] Eoin L. Brodie,et al. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.
[18] D. Allison,et al. Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.
[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] Ying Gao,et al. Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences , 2022 .
[21] Bjarne Stroustrup,et al. C++ Programming Language , 1986, IEEE Softw..
[22] H. Hotelling. Analysis of a complex of statistical variables into principal components. , 1933 .
[23] David R. Riley,et al. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing , 2011, BMC Bioinformatics.
[24] M. Metzker. Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.
[25] Satwik Rajaram,et al. NeatMap - non-clustering heat map alternatives in R , 2010, BMC Bioinformatics.
[26] Susan P. Holmes,et al. phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data , 2011, Pacific Symposium on Biocomputing.
[27] L. Raskin,et al. PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets , 2012, PloS one.
[28] John M. Chambers,et al. Software for data analysis , 2008 .
[29] Brian E. Granger,et al. IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.
[30] Campbell O. Webb,et al. Picante: R tools for integrating phylogenies and ecology , 2010, Bioinform..
[31] Jean Thioulouse,et al. Simultaneous analysis of a sequence of paired ecological tables: A comparison of several methods , 2011, 1202.5473.
[32] R. Peng. Reproducible Research in Computational Science , 2011, Science.
[33] Z. Merali. Computational science: ...Error , 2010, Nature.
[34] J. Booth,et al. Resampling-Based Multiple Testing. , 1994 .
[35] R. Clarke,et al. Theory and Applications of Correspondence Analysis , 1985 .
[36] Victoria Stodden,et al. Reproducible Research Concepts and Tools for Cancer Bioinformatics , 2010 .
[37] William A. Walters,et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.
[38] Darrel C. Ince,et al. The case for open computer programs , 2012, Nature.
[39] Leland Wilkinson,et al. The Grammar of Graphics (Statistics and Computing) , 2005 .
[40] James R. Cole,et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..
[41] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[42] Friedrich Leisch,et al. Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis , 2002, COMPSTAT.
[43] James A. Foster,et al. mcaGUI: microbial community analysis R-Graphical User Interface (GUI) , 2012, Bioinform..
[44] N. Pace. A molecular view of microbial diversity and the biosphere. , 1997, Science.
[45] R. Knight,et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex , 2008, Nature Methods.
[46] S. S. Young,et al. Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment , 1993 .
[47] Nick Barnes. Publish your computer code: it is good enough , 2010, Nature.
[48] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[49] C. Braak. Canonical Correspondence Analysis: A New Eigenvector Technique for Multivariate Direct Gradient Analysis , 1986 .
[50] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[51] Robert Gentleman,et al. Statistical Applications in Genetics and Molecular Biology , 2005 .
[52] Robert Gentleman,et al. Reproducible Research: A Bioinformatics Case Study , 2005, Statistical applications in genetics and molecular biology.
[53] W. Ludwig,et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.
[54] S. Holmes,et al. Bootstrapping Phylogenetic Trees: Theory and Methods , 2003 .
[55] Jonathan A. Eisen,et al. PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data , 2011, PLoS Comput. Biol..
[56] 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.
[57] R. Fleischmann,et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.
[58] M. Hill,et al. Detrended correspondence analysis: An improved ordination technique , 2004, Vegetatio.
[59] M. Greenacre. Correspondence analysis in practice , 1993 .
[60] James A. Foster,et al. OTUbase: an R infrastructure package for operational taxonomic unit data , 2011, Bioinform..
[61] R. Knight,et al. Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data , 2009, The ISME Journal.
[62] P. Bork,et al. Enterotypes of the human gut microbiome , 2011, Nature.
[63] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[64] Andreas Wilke,et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome , 2012, GigaScience.
[65] Rick L. Stevens,et al. Unlocking the potential of metagenomics through replicated experimental design , 2012, Nature Biotechnology.
[66] Edward R. Tufte,et al. The Visual Display of Quantitative Information , 1986 .
[67] Austin G. Davis-Richardson,et al. PANGEA: pipeline for analysis of next generation amplicons , 2010, The ISME Journal.
[68] H. L. Sanders,et al. Marine Benthic Diversity: A Comparative Study , 1968, The American Naturalist.
[69] Alfred M. Spormann,et al. W1926 Shifts in Luminal and Mucosal Microbial Communities Associated With an Experimental Model of Irritable Bowel Syndrome , 2010 .
[70] Gábor Csárdi,et al. The igraph software package for complex network research , 2006 .
[71] Mark Bailey,et al. The Grammar of Graphics , 2007, Technometrics.
[72] John M. Chambers,et al. Software for Data Analysis: Programming with R , 2008 .
[73] Alexander V. Alekseyenko,et al. Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data , 2011, Pacific Symposium on Biocomputing.
[74] Daniel P. Faith,et al. Compositional dissimilarity as a robust measure of ecological distance , 1987, Vegetatio.
[75] David L Donoho,et al. An invitation to reproducible computational research. , 2010, Biostatistics.
[76] M. Kenward,et al. An Introduction to the Bootstrap , 2007 .
[77] J. Ioannidis. Why Most Published Research Findings Are False , 2005, PLoS medicine.
[78] Hadley Wickham,et al. The Split-Apply-Combine Strategy for Data Analysis , 2011 .
[79] Andreas Wilke,et al. phylogenetic and functional analysis of metagenomes , 2022 .
[80] M. Adams,et al. Shotgun Sequencing of the Human Genome , 1998, Science.
[81] Roger D Peng,et al. Reproducible research and Biostatistics. , 2009, Biostatistics.
[82] J. Gower. Some distance properties of latent root and vector methods used in multivariate analysis , 1966 .