Identification of Periodically Expressed Genes

The GeneCycle package implements the approaches of Wichert et al. (2004), Ahdesmaki et al. (2005) and Ahdesmaki et al. (2007) for detecting periodically expressed genes from gene expression time series data.

The web supplement for the BMC Bioinformatics publication 6:117 can be found here (download Matlab implementation here). The web supplement (including a Matlab implementation) for the BMC Bioinformatics publication 8:233 can be found here.

Version: 1.1.1

Authors: Miika Ahdesmäki, Konstantinos Fokianos, and Korbinian Strimmer.

Documentation and Installation:

• Help pages and release history.
• Example sessions:
  • Finding periodically expressed genes in Caulobacter
  • R script reproducing the results in Table 2 of Wichert et al. (2004)
• Link to CRAN page of GeneCycle package.
• For network install, enter at R command prompt: install.packages("GeneCycle", dependencies=TRUE)

Papers:

• Wichert, S., K. Fokianos, and K. Strimmer. 2004. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 20: 5-20. (reprint)
• Ahdesmäki, M., Lähdesmäki, H., Pearson, R., Huttunen, H., and Yli-Harja o. 2005. Robust detection of periodic time series measured from biological systems. BMC Bioinformatics 6: 117. (reprint)
• Ahdesmäki, M., Lähdesmäki, H., Gracey, A., Shmulevich, I., and Yli-Harja O. 2007. Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics 8: 233. (reprint)

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