Opm: An R package for analysing OmniLog® phenotype microarray data

Bioinformatics

Volumn 29, Issue 14, 2013, Pages 1823-1824

  Vaas, Lea A I ^a   Sikorski, Johannes ^b   Hofner, Benjamin ^c   Fiebig, Anne ^b   Buddruhs, Nora ^b   Klenk, Hans Peter ^b   Göker, Markus ^b  

^a CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; PHENOTYPE; ARTICLE;

PHENOTYPE; SOFTWARE;

EID: 84880221612     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt291     Document Type: Article

References (16)

1. BiOLOG Inc. (2009) Converter, File Management Software, Parametric Software, Phenotype MicroArray, User Guide, Part 90333.
2. Biolog Inc., Hayward. Bochner, B.R. (2009) Global phenotypic characterization of bacteria. FEMS Microbiol. Rev., 33, 191-205.
3. Bochner, B. et al. (2001) Phenotype microarrays for high throughput phenotypic testing and assay of gene function. Genome Res., 11, 1246-1255.
4. Chambers, J. (1998) Programming with Data. Statistics and Computing. Springer, New York.
5. Eilers, P.H.C. et al. (1996) Flexible smoothing with B-splines and penalties. Stat. Sci., 11, 89-121.
6. T). Stand. Genomic Sci., 7, 440-448.
7. Goloboff, P.A. et al. (2008) TNT, a free program for phylogenetic analysis. Cladistics, 24, 774-786.
8. Hothorn, T. et al. (2008) Simultaneous inference in general parametric models. Biometr. J., 50, 346-363.
9. Kahm, M. et al. (2010) Grofit: fitting biological growth curves with R. J. Stat. Soft., 33, 1-21.
10. Montero-Calasanz, M.C. et al. (2012) Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. A. van Leeuw. J. Microb., 103, 449-456.
11. R Development Core Team. (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
12. Sarkar, D. (2008) Lattice: Multivariate Data Visualization with R. Springer, New York.
13. Stamatakis, A. et al. (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456-463.
14. Swofford, D. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland.
15. Vaas, L.A.I. et al. (2012) Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One, 7, e34846.
16. Wood, S.N. (2006) Generalized Additive Models: An Introduction with R. Chapman and Hall/CRC Press, Boca Raton.