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h T; L5 C# \; I2 khttps://www.biostars.org/p/164929/3 @# W1 V4 V5 j- D/ t# i6 w( }% v
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BeadScan: Analysing data from Illumina BeadArrays
0 |% e% z1 N O9 W+ }BisReadMapper: Library-free methylation sequencing with bisulfite padlock , t7 o1 ?/ _; B q
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner
7 t! Q' l V# \6 w/ fBSMAP: Probably the most widely used wild-card bisulphite aligner+ Y5 H- W; j3 B7 q0 e4 F$ ^$ F
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
% S. g1 d+ B& I& b4 uComBat: R script for correcting known or suspected batch effects # `8 C$ n* K$ O( d
DMAP: differential methylation analysis package for RRBS and WGBS data.
" b6 d. V1 c0 ^) c! |0 t8 x) O& `GenomeStudio: GenomeStudio Methylation Module v1.8, F3 i4 f+ J$ [; I
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
) h( X9 y+ B3 j; W) bisva: R package for batch effect correction using an algorithm& b/ P8 C: A- x
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2 - f s* A- ?5 J$ `8 C2 n0 C- i4 x/ ]
methylumi: R/Bioconductor package for Infinium data normalization/ M: z' e; X- i9 I/ D
minfi: R/Bioconductor package for Infinium data normalization, analysis
. T9 u! w7 C$ CPash: Wild-card bisulphite aligner included in a general-purpose alignment tool
- p' F2 V: f' j3 O9 Y$ X/ k( V' xRMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool& [6 ^4 |( Y5 v& R
RnBeads: R package providing a software pipeline for Infinium data normalization,6 }0 U$ U- p/ K% ^1 }+ T7 D
RRBSMAP: Variant of BSMAP that is specialized on reduced-representation& ^4 q ~, F7 @" S/ B8 F
segemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool2 S) ~* Y% ?8 u- K& z
SVA: R/Bioconductor package for correcting batch effects9 T& S. a5 |& ]1 [6 O
methyLiftover: cross-platform DNA methylation data integration4 _: N$ }! R6 g9 _, k8 a5 R, M$ K
dariober'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
