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' m( d4 y/ W4 L$ @7 `" ?% `https://www.biostars.org/p/164929/
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BeadScan: Analysing data from Illumina BeadArrays
- c: u+ d7 p: i# [( U/ [BisReadMapper: Library-free methylation sequencing with bisulfite padlock 9 H" @8 c. K3 }- x) M
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner$ `) b) a4 k( K& h: `6 s
BSMAP: Probably the most widely used wild-card bisulphite aligner* f, f* e2 V l. T$ o6 @ u
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.' `' o5 X9 R$ ?% V. Z' r& `
ComBat: R script for correcting known or suspected batch effects
( K8 @/ y( }4 ^9 d! k* iDMAP: differential methylation analysis package for RRBS and WGBS data.& U x7 a% ?8 L X3 q
GenomeStudio: GenomeStudio Methylation Module v1.81 e* X9 g. |9 E3 s1 E$ v
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose( Z( w$ X) k5 [1 d5 A
isva: R package for batch effect correction using an algorithm* o( x6 X- `7 `* B3 ~
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 7 k) V b; @# d; P4 U
methylumi: R/Bioconductor package for Infinium data normalization! p9 d0 ]9 d* }% }7 _+ B
minfi: R/Bioconductor package for Infinium data normalization, analysis
* [8 x F1 l% k' Q9 FPash: Wild-card bisulphite aligner included in a general-purpose alignment tool 3 C4 s; Y9 |: D
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
9 j w- @& v' Q# S" A( PRnBeads: R package providing a software pipeline for Infinium data normalization,+ Q% P F4 T1 O( Y! q' D5 A: ^
RRBSMAP: Variant of BSMAP that is specialized on reduced-representation3 G' W* K' G, K ]# }5 D
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool
& b( I9 S% c3 v. jSVA: R/Bioconductor package for correcting batch effects
" ]# }" S! [6 k- z) K$ _0 ^( H- jmethyLiftover: cross-platform DNA methylation data integration
% s1 r1 j+ ? ]8 i$ {! o Fdariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
