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https://www.biostars.org/p/164929/
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/ Y& v0 \% r$ |# l( a2 N* JBeadScan: Analysing data from Illumina BeadArrays$ V* T* R. C* u+ l
BisReadMapper: Library-free methylation sequencing with bisulfite padlock 8 z$ s+ m/ w* b! u6 Y: H
BRAT: Highly configurable and well-documented three‑letter bisulphite aligner
9 w. g; Y3 @/ O, I0 IBSMAP: Probably the most widely used wild-card bisulphite aligner/ i7 ?% r+ N$ `( [
BSmooth is a pipeline for analyzing WGBS data: aligning, quality control, and identifying DMRs.
" K, K& k: k6 @, c3 UComBat: R script for correcting known or suspected batch effects 6 Z2 G" \3 A( _, q6 J
DMAP: differential methylation analysis package for RRBS and WGBS data.: i, @+ x$ M+ [( V; ?& v/ N
GenomeStudio: GenomeStudio Methylation Module v1.8/ [" U, S3 \4 D5 _ w
GSNAP: Wild-card bisulphite aligner included in a widely used general-purpose
. M5 z) {& ]4 uisva: R package for batch effect correction using an algorithm8 ~7 ~7 _2 B5 t
MethylCoder: Three‑letter bisulphite aligner that can be used with either Bowtie and Bowtie2
P( @- R- e5 a* X: L& c2 Amethylumi: R/Bioconductor package for Infinium data normalization
( u& }, g6 }6 c& ]8 }' k, T/ }; N6 Nminfi: R/Bioconductor package for Infinium data normalization, analysis
$ E6 n" z+ ?9 Z% A) CPash: Wild-card bisulphite aligner included in a general-purpose alignment tool 4 L2 F! r3 X* q8 f% t" o
RMAP: Wild-card bisulphite aligner included in a general-purpose alignment tool
) V: ^4 O& A eRnBeads: R package providing a software pipeline for Infinium data normalization,
, L# [7 l% N5 v* W5 X8 i* S# uRRBSMAP: Variant of BSMAP that is specialized on reduced-representation
7 {1 W* u, B- [# {* bsegemehl: Wild-card bisulphite aligner included in a general-purpose alignment tool
- M8 M# H# Q* |+ PSVA: R/Bioconductor package for correcting batch effects
- Y+ H( o4 q# BmethyLiftover: cross-platform DNA methylation data integration' e% M" Z7 {5 `( y" ] v9 n
dariober's methylation-cafe: https://github.com/dariober/bioinformatics-cafe5 n1 Q5 l9 Q, F3 W {! E
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发表于 2016-4-25 02:29
发表于 2016-4-25 09:30
