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.

Miika Ahdesmaki, Konstantinos Fokianos, and Korbinian Strimmer.
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 GeneCycle package implements the approaches of Wichert
et al. (2004) <doi.org/10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <DOI:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.

The GeneCycle package implements the approaches of Wichert
et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.

person("Yinglei", "Lai", , "ylai@gwu.edu", role = c("aut", "cre"))
Implementation of several generalized F-statistics. The
current version includes a generalized F-statistic based on the
flexible isotonic/monotonic regression or order restricted hypothesis
testing. Based on: Y. Lai (2011) <doi:10.1371/journal.pone.0019754>.

This package implements several generalized F-statistics.
The current version includes a generalized F-statistic based on
the flexible isotonic/monotonic regression or order restricted
hypothesis testing.

Bayesian calculation of gene-specific FST from genomic SNP data
GeneFeST is a genome scan method to detect outlier loci (genes) which are under balancing or directional selection.

Relevance or Dependency network and signaling pathway discovery
The package implements a two-stage algorithm to screen co-expressed
gene paris with controlled FDR and MAS. The packages also constructs relevance
networks and clusters co-expressed genes (both similarly co-expressed and transitively
co-expressed)