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+ Z1 {% g' d" x7 j& Nhttps://www.biostars.org/p/164929/. V, J8 ?+ k* b0 e M
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2 u! N4 L b( J1 r6 oBeadScan: Analysing data from Illumina BeadArrays% p# I7 q% Y" G7 J2 h$ j
BisReadMapper: Library-free methylation sequencing with bisulfite padlock & U( B# l4 i X3 C: g
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner- L6 I) b4 q# n0 B# A7 B
BSMAP: Probably the most widely used wild-card bisulphite aligner
- p& d; Q$ U/ l0 b& x; FBSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.' `6 {& i" P6 \( n7 g& |
ComBat: R script for correcting known or suspected batch effects
. r1 b0 O k) jDMAP: differential methylation analysis package for RRBS and WGBS data.
; u7 d. c# K& z* u0 f) [1 o% oGenomeStudio: GenomeStudio Methylation Module v1.8( q3 _! \! g, w+ z
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose L3 l9 q! h( m! C* G( E. u: F
isva: R package for batch effect correction using an algorithm& N0 J" @! D2 w) U) q9 h
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2
9 r r L+ w4 x, ^methylumi: R/Bioconductor package for Infinium data normalization5 G7 {& c( ~& a2 ^$ h" ~0 ]
minfi: R/Bioconductor package for Infinium data normalization, analysis& p$ A" b- t% _. }8 I1 b* D* Z$ J
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool
& m+ l9 \! @4 q" a6 E8 W( x: m' cRMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool0 g, e7 r& \) G5 R! q' v1 l
RnBeads: R package providing a software pipeline for Infinium data normalization,2 S% u7 o% g" v* I; C
RRBSMAP: Variant of BSMAP that is specialized on reduced-representation- `( d" }/ k( F8 {4 g* u
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool: y4 A' X6 @! z7 P5 c/ m
SVA: R/Bioconductor package for correcting batch effects7 W, d; Z& H6 R7 d6 O5 D" _, }% ?
methyLiftover: cross-platform DNA methylation data integration" \' o/ x/ \5 @1 J! @& [
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe7 r4 h. @; m9 j: S6 P2 Q2 M
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
