Visualization and statistical comparisons of microbial communities using R packages on phylochip data

Pacific Symposium on Biocomputing 2011, PSB 2011

Volumn , Issue , 2011, Pages 142-153

  Holmes, Susan ^a   Alekseyenko, Alexander ^b   Timme, Alden ^a   Nelson, Tyrrell ^d   Pasricha, Pankaj Jay ^c   Spormann, Alfred ^c  

^a STANFORD UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Stanford University   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Hypergeometric Test; PhyloChip; Phylogenetic Tree; projections; Quality Control; R

Indexed keywords

HYPERGEOMETRIC TEST; PHYLOCHIP; PHYLOGENETIC TREES; PROJECTIONS; R;

QUALITY CONTROL;

DATA VISUALIZATION;

RNA 16S;

ANIMAL; ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; GENETICS; HUMAN; IRRITABLE COLON; METAGENOME; METAGENOMICS; MICROBIOLOGY; MULTIVARIATE ANALYSIS; PHYLOGENY; RAT; STATISTICAL ANALYSIS; STATISTICS;

ANIMALS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; HUMANS; IRRITABLE BOWEL SYNDROME; METAGENOME; METAGENOMICS; MULTIVARIATE ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; RATS; RNA, RIBOSOMAL, 16S; SOFTWARE;

EID: 84872896954     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. T. A. Nelson, S. Holmes, A. V. Alekseyenko, M. Shenoy, T. DeSantis, C. Wu, G. L. Anderson, J. Sonnenburg, P. J. Pasricha and A. Spormann, Phylochip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity, Submitted.
2. T. King, M. Elia and J. Hunter, The Lancet (Jan 1998).
3. E. Malinen, T. Rinttila, K. Kajander and J. Matto, The American journal of Gastroenterology 100, 373 (Jan 2005).
4. A. Kassinen, L. Krogius-Kurikka and H. Makivuokko, Gastroenterology (Jan 2007).
5. K. H. Wilson, W. J. Wilson, J. L. Radosevich, T. Z. DeSantis, V. S. Viswanathan, T. A. Kuczmarski and G. L. Andersen, Appl. Environ. Microbiol. 68, 2535 (2002).
6. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. H. Yang and J. Zhang, Genome Biology 5, p. R80 (Jan 2004).
7. R. A. Irizarry, L. Gautier, W. Huber and B. Bolstad, makecdfenv 1.18 (2009), http://cran. r-project.org/doc/packages/makecdfenv.pdf.
8. W. Huber, A. von Heydebreck, H. Sultmann, A. Poustka and M. Vingron, Bioinformatics 18 Suppl 1, S96 (Jan 2002).
9. S. N. Evans and F. A. Matsen, arXiv q-bio.PE (Jan 2010).
10. M. Hamady, C. Lozupone and R. Knight, The ISME Journal (Jan 2009).
11. E. Purdom, Annals of Applied Statistics .
12. B. Durbin, J. Hardin, D. Hawkins and D. Rocke, Bioinformatics 19, 1360 (2003).
13. R. Ihaka and R. Gentleman, Journal of Computational and Graphical Statistics 5, 299 (1996).
14. D. Chessel, A. Dufour and J. Thioulouse, R News 4, 5 (2004).
15. J. Qin, R. Li, J. Raes, M. Arumugam, K. er Solvsten Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. ce Levenez, T. Yamada, D. R. Mende, J. Li, J. Xu, S. Li, D. Li, J. Cao, B. Wang, H. Liang, H. Zheng, Y. ong Xie, J. Tap, P. Lepage, M. Bertalan, J.-M. Batto, T. orben Hansen, D. L. Paslier, A. Linneberg, H. B. Nielsen, E. P. tier, P. Renault, T. Sicheritz-Ponten, K. Turner, H. Zhu, C. ang Yu, S. Li, M. Jian, Y. Zhou, Y. Li, X. Zhang, S. gang Li, N. Qin, H. Yang, J. Wang, S. Brunak, J. D. a nd Francisco Guarner, K. Kristiansen, O. Pedersen, J. Parkhill, J. Weissenbach, M. Consortium, P. Bork, S. D. Ehrlich and J. Wang, Nature 464, 59 (Mar 2010).
16. E. Paradis, Ape (analysis of phylogenetics and evolution) v1.8-2 (2006), http://cran. r-project.org/doc/packages/ape.pdf.
17. B. Efron, R. Tibshirani and R. Tibshirani, An introduction to the bootstrap (Chapman & Hall/CRC, 1993).
18. E. Paradis, J. Claude and K. Strimmer, Bioinformatics 20, 289 (2004).
19. D. Sarkar, lattice: Lattice Graphics, (2009). R package version 0.17-26.
20. I. Rivals, L. Personnaz, L. Taing and M.-C. Potier, Bioinformatics 23, 401 (Feb 2007).
21. S. Kembel, P. Cowan, M. Helmus, W. Cornwell, H. Morlon, D. Ackerly, S. Blomberg and C.Webb, Bioinformatics 26, 1463 (2010).
22. K. S. Pollard, H. N. Gilbert, Y. Ge, S. Taylor and S. Dudoit, multtest: Resampling-based multiple hypothesis testing, (2010). R package version 2.4.0.
23. J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, R. G. O'Hara, G. L. Simpson, P. Solymos, M. H. H. Stevens and H. Wagner, vegan: Community Ecology Package, (2010). R package version 1.17-0.