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https://www.biostars.org/p/164929/' d4 Z( U/ I+ P; d7 m7 ~
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& u, |2 \$ h% L' r ^BeadScan: Analysing data from Illumina BeadArrays
8 q" v* P: K2 S7 i ]4 D3 Z4 NBisReadMapper: Library-free methylation sequencing with bisulfite padlock " m7 `$ T! {, |7 B! ?
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner
1 L! b$ K M, f$ b9 ^. KBSMAP: Probably the most widely used wild-card bisulphite aligner* ~! M% S7 K; D
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
; N& B# O. f0 [+ ~ComBat: R script for correcting known or suspected batch effects ' `: k, v, J( ^
DMAP: differential methylation analysis package for RRBS and WGBS data., h* s" v P J7 O# ]9 B
GenomeStudio: GenomeStudio Methylation Module v1.8
; v4 l$ D H" C9 T' l- z, h: ^GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose4 S% N& O- S" I, w+ ]0 } W
isva: R package for batch effect correction using an algorithm
% l2 N/ i6 w/ H. U9 S3 ZMethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2
G; P& }$ z8 U3 Rmethylumi: R/Bioconductor package for Infinium data normalization
6 b0 X; W2 h+ ominfi: R/Bioconductor package for Infinium data normalization, analysis
& `2 d1 m5 n8 q% q0 }4 T; `) xPash: Wild-card bisulphite aligner included in a general-purpose alignment tool & S* L+ g6 u7 P- ?+ d( B9 y
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool) G1 D K" z5 B% Q6 W! v/ X* t7 C
RnBeads: R package providing a software pipeline for Infinium data normalization,
( Y6 N, W9 q6 s! x) }RRBSMAP: Variant of BSMAP that is specialized on reduced-representation
. z! X& R: ?2 T V/ j, m7 Rsegemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool- R7 V% B: `- R- ?- ^+ U" X
SVA: R/Bioconductor package for correcting batch effects* u/ T# [/ O9 }. k, p, M. ^4 Q
methyLiftover: cross-platform DNA methylation data integration
% q" n, |- v6 z: N# edariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe* c+ k% } A, W6 i& f
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
