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BeadScan: Analysing data from Illumina BeadArrays
BisReadMapper: Library-free methylation sequencing with bisulfite padlock
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner
BSMAP: Probably the most widely used wild-card bisulphite aligner
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
ComBat: R script for correcting known or suspected batch effects
DMAP: differential methylation analysis package for RRBS and WGBS data.
GenomeStudio: GenomeStudio Methylation Module v1.8
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
isva: R package for batch effect correction using an algorithm
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2
methylumi: R/Bioconductor package for Infinium data normalization
minfi: R/Bioconductor package for Infinium data normalization, analysis
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
RnBeads: R package providing a software pipeline for Infinium data normalization,
RRBSMAP: Variant of BSMAP that is specialized on reduced-representation
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool
SVA: R/Bioconductor package for correcting batch effects
methyLiftover: cross-platform DNA methylation data integration
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe
metilene for DMR (Fast and Sensitive: better than MOABS and Bsmooth)http://www.bioinf.uni-leipzig.de/Software/metilene/Downloads/
scLVM: single-cell RNA-seq heterogeneity source deconvolution
methpipe: http://smithlabresearch.org/software/methpipe/
Bis-SNP: http://people.csail.mit.edu/dnaase/bissnp2011/
COMETs: Information recovery from low coverage whole-genome bisulfite sequencing
HMMcopy: copy number estimations for whole genome data with GC and mappability correction
BS-SNPer: SNP calling in bisulfite-seq data
