9 N, j+ j8 W2 S% b$ \/ N3 U% u) F1 O4 {+ g
BeadScan: Analysing data from Illumina BeadArrays- ]' z+ u0 ?4 z% q
BisReadMapper: Library-free methylation sequencing with bisulfite padlock . }# r5 t: a$ b" e: D$ g" u5 e
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner8 E( {( A& t" D8 J, \
BSMAP: Probably the most widely used wild-card bisulphite aligner9 V7 J0 f; \2 w
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs." ^# d) Y4 O0 k3 v. P. e" P
ComBat: R script for correcting known or suspected batch effects 1 O; D4 l6 E9 _
DMAP: differential methylation analysis package for RRBS and WGBS data.) O$ \8 i1 B3 C% t0 q" e) J
GenomeStudio: GenomeStudio Methylation Module v1.80 H3 ~, o& d3 ?, w# [
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose5 Y7 v) g; e2 ^5 ?
isva: R package for batch effect correction using an algorithm" W& U7 I6 I% k
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 ( Q8 V( G/ E1 H7 l# D
methylumi: R/Bioconductor package for Infinium data normalization 2 ~: m0 l& ~+ N9 sminfi: R/Bioconductor package for Infinium data normalization, analysis ) y* I) _( V, E6 z! N- W1 vPash: Wild-card bisulphite aligner included in a general-purpose alignment tool ! [/ O, t* M e3 v2 y' sRMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool 6 D0 d+ v. O) x. _0 {RnBeads: R package providing a software pipeline for Infinium data normalization, , X$ c: l, |1 O/ X" k$ kRRBSMAP: Variant of BSMAP that is specialized on reduced-representation 5 e' s: I$ ^1 P+ _1 Gsegemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool. h2 D& t& `- S
SVA: R/Bioconductor package for correcting batch effects0 G! r8 R! s% `9 L1 U
methyLiftover: cross-platform DNA methylation data integration* P7 t6 v# O& }6 U# [% M
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe $ T9 U6 _* E9 Z* a% k) \. _* j作者: yeshch 时间: 2016-4-25 09:30