R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP
(>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology
(>= 2.0)

Simulate, model, and display data from a time-course microarray
experiment with periodic gene expression
Timothy McMurry <tmcmurry@depaul.edu>, Arthur Berg
<berg@psu.edu>
Fit models for periodic gene expression to time-course
microarray data in a normal mixture model framework with mean
approximated by a truncated Fourier series and covariance
structure modeled by an ARMA(p,q) process.  Estimation is
performed with the EM algorithm.

Retrieves Gene Expression Dataset from GEO Code and Platform ID
person("Davide", "Chicco", email = "davidechicco@davidechicco.it",
role = c("aut", "cre"))
A function that reads in the GEO code and the platform ID of a gene expression dataset, retrieves its data from GEO, (optional) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293,  GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Retrieves Gene Expression Dataset and Gene Symbols from GEO Code
A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optional) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293,  GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293,  GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, Springer Protocols, New York City, New York, USA, 2021. In press.
BiocManager, xml2, Biobase, annotate, GEOquery, markdown,
R.utils