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DNA甲基化分析软件汇总

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发表于 2016-4-25 02:29 |显示全部帖子
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https://www.biostars.org/p/164929/
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BeadScan: Analysing data from Illumina BeadArrays' o5 u) C6 K  q6 i  R6 V
BisReadMapper: Library-free methylation sequencing with bisulfite padlock ; m# D; U8 Q* \* Z3 e
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner! m- A8 C  u/ S. @
BSMAP: Probably the most widely used wild-card bisulphite aligner
/ l9 X, |- w  ~# l2 MBSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.6 P9 f' n  f$ J. w: n/ T
ComBat: R script for correcting known or suspected batch effects
5 P1 A  ~) i/ W; K2 I" p7 }DMAP: differential methylation analysis package for RRBS and WGBS data.
6 D" g/ N4 M6 o2 x1 `GenomeStudio: GenomeStudio Methylation Module v1.88 m$ P" o+ E, o* P6 `
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
" ?# C) T/ E5 Y& ?5 U3 f. Pisva: R package for batch effect correction using an algorithm
; y" z/ `; ^; E7 s- a4 L  d# t  eMethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 + Z$ P( v- ?# v4 ~* h+ k
methylumi: R/Bioconductor package for Infinium data normalization0 S: X$ Z& q! J' p! j6 {$ \2 u
minfi: R/Bioconductor package for Infinium data normalization, analysis  S# a$ O; D/ a; S
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool : E- e+ {6 g' Y5 e: S7 ]5 m2 F
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
3 v- k5 ?& @4 j. ]6 }2 |RnBeads: R package providing a software pipeline for Infinium data normalization,
5 \) `0 S1 k/ q, g" j$ p0 }1 kRRBSMAP: Variant of BSMAP that is specialized on reduced-representation3 V7 Q9 z$ ]9 Q2 O# z, e, F# b
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool7 }9 M) @. P3 v+ P9 P8 p
SVA: R/Bioconductor package for correcting batch effects
6 b: J& y% N# x! |6 ]methyLiftover: cross-platform DNA methylation data integration2 x: j  N- V- S4 E
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe& R8 m2 N% ]" z' K
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发表于 2016-4-25 09:30 |显示全部帖子
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发表于 2016-4-25 10:12 |显示全部帖子
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