* S, u6 p/ f2 ^ EBeadScan: Analysing data from Illumina BeadArrays 8 c8 T6 x1 I0 U4 d* v( Q# jBisReadMapper: Library-free methylation sequencing with bisulfite padlock x' L8 y. ~8 U t0 y) mBRAT: Highly configurable and well-documented three‑letter bisulphite aligner. l/ i' s; W6 F
BSMAP: Probably the most widely used wild-card bisulphite aligner( z2 ]( I6 K7 g" l* u$ U
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs. 8 R( m" Z4 O% A* k+ d0 [ComBat: R script for correcting known or suspected batch effects + b9 \: ]( l8 t* v
DMAP: differential methylation analysis package for RRBS and WGBS data. " C% ~% S0 h" x. Q. f' IGenomeStudio: GenomeStudio Methylation Module v1.8 3 ?* x7 N! s- N' X' h5 w: SGSNAP: Wild-card bisulphite aligner included in a widely used general-purpose* B, T" Q1 Y {5 f% c
isva: R package for batch effect correction using an algorithm 2 J! K$ M$ f7 A1 l6 O' ]# nMethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 , f0 O' t* _3 R' N) U
methylumi: R/Bioconductor package for Infinium data normalization Z' M* O, |; n! \4 B/ R$ ?6 Zminfi: R/Bioconductor package for Infinium data normalization, analysis 6 `9 G( b; [/ B$ jPash: Wild-card bisulphite aligner included in a general-purpose alignment tool ! _# \( O/ C/ v# Q) z" URMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool4 x7 @% g) i4 n: a! j( L0 a c
RnBeads: R package providing a software pipeline for Infinium data normalization, * ~8 R P* v* iRRBSMAP: Variant of BSMAP that is specialized on reduced-representation e( a5 T x F+ N
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool0 W2 ~3 h1 L: E( f+ N7 D T( y
SVA: R/Bioconductor package for correcting batch effects & I& u$ Z, p& m4 ?+ A2 PmethyLiftover: cross-platform DNA methylation data integration) }" Q9 Z' a* s/ _
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe+ l4 c I C7 C1 l: X0 y# O% c 作者: yeshch 时间: 2016-4-25 09:30