Table 2.
Software for the analysis of DNA methylation data
| Software | Purpose | URL | Reference |
|---|---|---|---|
| charm | Modified Loess normalization; Modified normal-exponential convolution; subset quantile normalization; estimate absolute DNA methylation using empirical Bayes |
http://www.bioconductor.org | Aryee et al. (2010) |
| HELP | Quantile normalization by fragment length for data generated using HELP assay | http://www.bioconductor.org | Thompson et al. (2010) |
| beadarray | For Illumina BeadArray data | http://www.bioconductor.org | Dunning et al. (2007) |
| lumi | For Illumina BeadArray data | http://www.bioconductor.org | Du et al. (2008) |
| MEDME | Estimate absolute DNA methylation from MeDIP study | http://www.bioconductor.org | Pelizolla et al. (2008) |
| MEDIPS | Analysis of MeDIP-seq data, with functions useful for other types of enrichment (MBD-seq) or sequence data (ChIP-seq) | http://www.bioconductor.org | Chavez et al. (2010) |
| Batman | Estimate absolute DNA methylation from MeDIP study | http://tdblade.gurdon.cam.ac.uk/software/batman | Down et al. (2008) |
| RPMM | Cluster analysis of Illumina beta values | http://www.bioconductor.org | Houseman et al. (2008) |
| Circos | Visualization tool | http://mkweb.bcgsc.ca/circos | Krzywinski et al. (2009) |
| Repitools | Analysis of epigenomic data from enrichment-based microarrays | http://repitools.r-forge.rproject.org | Statham et al. (2010) |
| PASH 3.0 | Analysis of Bisulfite Sequence data | http://www.brl.bcm.tmc.edu/pash/pashDownload. rhtml | Coarfa et al. (2010) |
| edgeR | Analysis of Bisulfite Sequence data | http://www.bioconductor.org | Robinson et al. (2010a) |