Japan Bioinformatics

Simbiot contains functions to perform CNV analysis on data generated using Affymetrix and Illumina SNP microarrays.  The analysis is done using Bioconductor (Gentleman, Carey et al. 2004) snapCGH (Marioni, Thorne et al. 2006; Smith, Marioni et al. 2006).  A total of five copy number analysis algorithms are available including two versions of Hidden Markov Models.

 

References

Gentleman, R. C., V. J. Carey, et al. (2004). “Bioconductor: open software development for computational biology and bioinformatics.” Genome Biol 5(10): R80.

Marioni, J. C., N. P. Thorne, et al. (2006). “BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data.” Bioinformatics 22(9): 1144-6.

Smith, M. L., J. C. Marioni, et al. (2006). “snapCGH: Segmentation, Normalization and Processing of aCGH Data Users’ Guide.” Bioconductor.