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https://www.biostars.org/p/164929/8 h+ T" y4 `. _; N$ S' ]) V
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BeadScan: Analysing data from Illumina BeadArrays. |" L, d4 Z, w$ Y
BisReadMapper: Library-free methylation sequencing with bisulfite padlock
, `9 H: d# O( J6 h; Y8 ABRAT: Highly configurable and well-documented three‑letter bisulphite aligner8 d" Y F! H6 V$ B- [5 }* U
BSMAP: Probably the most widely used wild-card bisulphite aligner
( b: b- k" f. z N' y4 rBSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
! ?9 z N! P- u+ K) Y4 g0 r. [0 P% xComBat: R script for correcting known or suspected batch effects - X7 G7 T6 m& I: k) U0 B
DMAP: differential methylation analysis package for RRBS and WGBS data.
/ C3 M0 o } K. `6 ~+ y' i3 BGenomeStudio: GenomeStudio Methylation Module v1.8: u3 \% n: P$ w5 o. q. i
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
* b* s* T# ]9 cisva: R package for batch effect correction using an algorithm
9 Y9 x8 R$ h# M! G: uMethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 " C! U7 y$ J4 {2 R: `) P
methylumi: R/Bioconductor package for Infinium data normalization
! X) H) Z/ \; t# Kminfi: R/Bioconductor package for Infinium data normalization, analysis) A/ }( C( `9 A/ ]* P$ Q( m
Pash: Wild-card bisulphite aligner included in a general-purpose alignment tool " m2 g2 v5 W5 J" E3 }% F* ^
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
2 x: V0 z# t& C- z( f5 @RnBeads: R package providing a software pipeline for Infinium data normalization,
& s& b/ k( m2 g8 A3 ^; G/ JRRBSMAP: Variant of BSMAP that is specialized on reduced-representation* x; {' F! [1 v4 w5 r
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool
" k, M7 W3 [+ g! r, SSVA: R/Bioconductor package for correcting batch effects
3 k$ D# }% t4 }$ X# S. e" E) OmethyLiftover: cross-platform DNA methylation data integration
/ k7 B& x& Q3 ^: y7 A, f' Hdariober'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
