The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic data.
Tools that extract phenotype alterations from transcriptomic data are important to improve the interpretation of biological studies. PATHChange is a statistical CRAN package designed to work with data downloaded from the Gene Expression Omnibus database (GEO) to determine differential pathway expression in comparative studies including control samples. In this paper we present details of the structure, implementation and an example of use of the package.
Department of Physics, Universidade Federal de Santa Maria, Avenida Roraima, 97105-900 Santa Maria, Brazil. Electronic address: carladriani@yahoo.com.br.
Carla A R S
CA
Fontoura
Department of Physics and Astronomy, Bologna University, Viale B. Pichat, 40123 Bologna, Italy. Electronic address: gastone.castellani@unibo.it.
Gastone
G
Castellani
Department of Physics, Universidade Federal de Santa Maria, Avenida Roraima, 97105-900 Santa Maria, Brazil. Electronic address: jcmombach@ufsm.br.
José C M
JC
Mombach
D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D059467:Transcriptome / Q000235:genetics*
CRAN package; Microarray; Pathway expression; R; RNA-seq