09/12/2020
Integrated R Packages
GEAP was developed in two languages:
- C# for graphical user interface, storage and file checking; and
- R for expression data set processing and statistical analyses.
The table below lists the most relevant R packages used by GEAP to perform tasks through R. The rgeap package is responsible for redirecting calls from C# to R, where some functions are imported from these external packages and adapted to the features in the main program.
| Package Name | External References | Usage |
|---|---|---|
| affy | Cite Link |
|
| affxparser | Cite Link | Collecting information from Affymetrix CEL file headers |
| arrayQualityMetrics | Cite Link | Quality analysis evaluation |
| beadarray | Cite Link |
|
| Biobase | Cite Link | Importing generic methods and classes used in microarray analyses (e.g., ExpressionSet) |
| BiocManager | Link | Installation and management of Bioconductor packages |
| Cairo | Link | Exporting graphics in PNG and SVG formats |
| devtools | Link |
|
| gcrma | Cite Link | Statistical treatment of Affymetrix raw data |
| illuminaio | Cite Link |
|
| limma | Cite Link |
|
| makecdfenv | Cite Link | Handling custom CDF annotations for Affymetrix microarrays |
| NanoStringNorm | Cite Link |
|
| oligo | Cite Link |
|
| openssl | Link | Implementation of safe C# ↔ R communication |
| plier | Cite Link | Statistical treatment of Affymetrix raw data |
| Rcpp | Link | C++ integration and implementation of optimized file processing functions |
| Rgraphviz | Cite Link | Plotting R graphs for Gene Ontology analysis results |
| topGO | Cite Link | Statistical algorithms for Gene Ontology analyses |