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https://www.biostars.org/p/164929/0 L/ z& z+ C4 [- Y4 _
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BeadScan: Analysing data from Illumina BeadArrays
5 ~7 _, h' ?/ ~. l3 A" ?BisReadMapper: Library-free methylation sequencing with bisulfite padlock
5 ~" X3 p W* e2 a. G( v6 t0 X# nBRAT: Highly configurable and well-documented three‑letter bisulphite aligner
+ k" H0 U' N; K! x) U) VBSMAP: Probably the most widely used wild-card bisulphite aligner7 m5 G& n/ J# z: ~
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
0 o/ P& \* B# Q. VComBat: R script for correcting known or suspected batch effects L: z Y0 P% ~% R! D
DMAP: differential methylation analysis package for RRBS and WGBS data.
" f- h3 F% C. c+ o- V( FGenomeStudio: GenomeStudio Methylation Module v1.8; l2 m X5 ] F3 y
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
) G+ D6 k4 H5 Q2 g. a6 w o& |isva: R package for batch effect correction using an algorithm
% i9 ~' E+ \( y8 E5 a2 V6 XMethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 " G' \- S1 p" v
methylumi: R/Bioconductor package for Infinium data normalization
9 R4 C$ Z& H2 W9 k8 L8 f. V/ @minfi: R/Bioconductor package for Infinium data normalization, analysis$ C/ j4 u9 x; D; f) O2 ^( i# h
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool
* |" F8 n }/ A; ^+ WRMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool: z7 D1 Y* x$ ?3 u) o) d
RnBeads: R package providing a software pipeline for Infinium data normalization,
8 J: e9 B; R$ H0 M) c1 LRRBSMAP: Variant of BSMAP that is specialized on reduced-representation
% E, P& H3 ?$ \1 h' ~, Ysegemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool+ y/ l* X* L$ f' L" b6 ]
SVA: R/Bioconductor package for correcting batch effects
# V+ E7 b: V8 f7 I8 i1 Y# \1 JmethyLiftover: cross-platform DNA methylation data integration
a: j" W7 o3 h2 j3 fdariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe# W6 W. p# ^, D+ m
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
