easyDifferentialGeneCoexpression: Easily Performs Differential Coexpression Analysis

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: 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/>.

Version: 0.9
Depends: R (≥ 4.0.0)
Imports: annotate, Biobase, diffcoexp, geneExpressionFromGEO, GEOquery, jetset, magrittr, R.utils, stringi, xml2
Suggests: knitr, rmarkdown
Published: 2021-12-08
Author: Davide Chicco ORCID iD [aut, cre]
Maintainer: Davide Chicco <davidechicco at davidechicco.it>
BugReports: https://github.com/davidechicco/easyDifferentialGeneCoexpression/issues
License: GPL-3
URL: https://github.com/davidechicco/easyDifferentialGeneCoexpression
NeedsCompilation: no
CRAN checks: easyDifferentialGeneCoexpression results

Documentation:

Reference manual: easyDifferentialGeneCoexpression.pdf
Vignettes: easyDifferentialGeneCoexpression

Downloads:

Package source: easyDifferentialGeneCoexpression_0.9.tar.gz
Windows binaries: r-devel: easyDifferentialGeneCoexpression_0.9.zip, r-release: easyDifferentialGeneCoexpression_0.9.zip, r-oldrel: easyDifferentialGeneCoexpression_0.9.zip
macOS binaries: r-release (arm64): not available, r-release (x86_64): not available, r-oldrel: not available
Old sources: easyDifferentialGeneCoexpression archive

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