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https://www.biostars.org/p/164929/" t4 A9 a5 F6 \& n- x; L
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& J9 @( j% ^/ J% C7 Q% f' EBeadScan: Analysing data from Illumina BeadArrays
6 a7 e# Z9 r4 y+ W! G, g! |0 `BisReadMapper: Library-free methylation sequencing with bisulfite padlock ' j1 A3 N9 C- \% n2 S3 v s _ d
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner7 ~% |9 Y/ i y9 y1 s
BSMAP: Probably the most widely used wild-card bisulphite aligner" V* x2 \$ f& U/ S- \0 @
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.2 w' O" E( u1 v. {. S$ V/ C
ComBat: R script for correcting known or suspected batch effects
) O7 g! j0 m- m+ A+ t6 b) g+ eDMAP: differential methylation analysis package for RRBS and WGBS data.
J- |) [: y) {GenomeStudio: GenomeStudio Methylation Module v1.8
: K; S8 X9 b6 `0 k, V6 jGSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
- R# b2 e4 w. `9 O/ y# K( Uisva: R package for batch effect correction using an algorithm+ R4 z9 R. Z* C- u# ~+ r
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 2 i8 Y- S+ u: r; \8 y
methylumi: R/Bioconductor package for Infinium data normalization
" b, L8 w) ~# S! r6 C8 Jminfi: R/Bioconductor package for Infinium data normalization, analysis3 {' E- N3 Z0 J9 y) T
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool - D0 v" x9 g# m, @, J
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool+ U. R) b* j9 _2 l4 ]
RnBeads: R package providing a software pipeline for Infinium data normalization, X* |- k: \% M7 R, p5 i7 f$ s8 v$ [) u
RRBSMAP: Variant of BSMAP that is specialized on reduced-representation2 ?7 ?- l7 s! R0 r
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool# n! ]/ O4 W6 [
SVA: R/Bioconductor package for correcting batch effects7 T# S$ i$ L4 [3 X) P
methyLiftover: cross-platform DNA methylation data integration
2 E* H0 U, S. P3 [, Wdariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe& u3 z! y7 W0 j7 ]8 a6 F4 l
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
