Table 5 Package dependencies

AffyCompatible

Annotation of Affymetrix microarrays

ArrayExpress

Access to the ArrayExpress online repository

crlmm

Genotyping of microarray SNP data

DESeq2

Processing of RNA-seq data

DMRcate

Statistical analysis of methylation data

edgeR

Statistical analysis of RNA-seq data

ff

Store large in-memory datasets on disk

limma

Statistical analysis of microarray RNA data

minfi

Import and normalization of microarray methylation data

mixOmics

Methods for integrative analysis of multi-omics data

MOFA

Integrative analysis by multi-omics factor analysis

MSnbase

Import of proteomics data

MultiDataSet

Data integration of multi-omics data

oligo

Import and normalization of microarray RNA data

RefFreeEWAS

Correction for cell type composition in methylation data

SNPRelate

Processing SNP data

snpStats

Statistical analysis of SNP data

SummarizedExperiment

Import of RNA-seq data

wateRmelon

Normalization of microarray methylation data