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https://www.biostars.org/p/164929/# L q% D5 X4 V: ]
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" p, [ g# P, X5 ]& i* B# h; mBeadScan: Analysing data from Illumina BeadArrays$ K6 t; w4 K4 N4 C, ~3 c) }
BisReadMapper: Library-free methylation sequencing with bisulfite padlock 6 A0 H/ y' ^+ Q
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner8 X/ e, s& _3 a3 v- v
BSMAP: Probably the most widely used wild-card bisulphite aligner
2 M4 M g7 N; g! m# r+ s3 D1 B( ?BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.+ t; p0 y6 a9 j* T2 P5 T. N
ComBat: R script for correcting known or suspected batch effects
% C Y3 @$ k* \4 \" q( VDMAP: differential methylation analysis package for RRBS and WGBS data.
3 O7 p( ~. f5 @- h: T! o) A OGenomeStudio: GenomeStudio Methylation Module v1.83 `; z- ?, E$ B. J
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose/ \. R& p( K# v8 u9 F
isva: R package for batch effect correction using an algorithm
& _- ^: l ^5 t5 X) ~MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 ( |3 `# b8 [9 B0 J2 p
methylumi: R/Bioconductor package for Infinium data normalization
: h+ f$ N, k: U3 \0 L8 _. E4 [minfi: R/Bioconductor package for Infinium data normalization, analysis) @' F8 l0 C, i l( l: ~0 @
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool . x6 Q4 h) h. c6 S6 O
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
* Z y, x) Q M* {RnBeads: R package providing a software pipeline for Infinium data normalization,
. B b# M, z) f7 U2 jRRBSMAP: Variant of BSMAP that is specialized on reduced-representation% h" a1 z8 q+ v1 @; c
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool8 `8 Z/ t2 |7 F% G9 k
SVA: R/Bioconductor package for correcting batch effects
' L( M$ ?' }% ]: c6 EmethyLiftover: cross-platform DNA methylation data integration$ s" _# v' @+ w! A5 z) o
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe1 ?/ u% i4 d8 @/ L8 N. S# L
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
