This package consists of modularized wrapper functions for multiple genomics analysis packages. It is designed for analysis of expression, methylation and/or genotyping data. All modules can also be used individually. E.g. for gene expression data, workflow is as follows: Illumina microarray data or custom microarray data are loaded into an Expressionet object and are normalised and QC-controlled. Limma package is used for differential expression analysis of all indicated group comparisons. Differential expressed genes are analysed for enriched GO terms, KEGG pathways and transcription factor binding sites using clusterProfiler and PWMEnrich. Principal component analysis and whole genome coexpression network analysis is performed using WGCNA and pcaGoPromoter packages.
|Author||Frank Ruehle [aut, cre]|
|Maintainer||Frank Ruehle <[email protected]>|
|Package repository||View on GitHub|
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