Table 2 Current typical platforms for methylation array data analysis
From: MADA: a web service for analysing DNA methylation array data
platform | system | installation | Interface | Â | Functions & tools | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
workflow | Preprocessing | DMP | DMR | Data visualization | Gene ontology analysis | Pathway analysis | Cluster analysis | ||||
Minfi [7] | Unix/Linux, Mac OS, Windows | R package manager | Command line | – | Funnorm, SWAN, Illumina, SQN | – | Bumphunter | Preprocessing | – | – | – |
ChAMP [8] | Unix/Linux, Mac OS, Windows | R package manager | Command line interface, GUI | √ | BMIQ.PBC SWAN, Funnorm,Combat | Limma | DMRcate, Bumphunter, ProbeLasso | Preprocessing, DMP/DMR/GO | √ | √ | – |
watermelon [18] | Unix/Linux, Mac OS, Windows | R package manager | Command line | – | Dasen, BMIQ, SWAN | – | – | – | – | – | – |
RnBeads [32] | Unix/Linux, Mac OS, Windows | R package manager | command line | √ | SWAN, Noob, Dasen | Limma |  | Preprocessing | √ | – | – |
ADMIRE [11] | Unix/Linux, Mac OS, Windows | not needed | Web server/Command line | – | Funnorm, SWAN, Illumina, SQN | – | A statistical testing | Preprocessing, DMR | √ | – | – |
Methylumi [16] | Unix/Linux, Mac OS, Windows | R package manager | command line | – | Noob | – | – | Preprocessing | – | – | – |
missMethyl [28] | Unix/Linux, Mac OS, Windows | R package manager | Command line interface | – | SWAN | Limma | – | Preprocessing DMP | √ | √ | – |
MADA | Unix/Linux, Mac OS, Windows | not needed/compilation from script | Web server/local web server | √ | BMIQ, PBC, Noob, Funnorm, SWAN, Illumina, SQN, RAW, Combat | Limma | DMRcate, Bumphunter, ProbeLasso, Seqlm | Preprocessing DMP/DMRGO/KEGG | √ | √ | √ |