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oxBS-seq/TAB-seq/fCAB-seq/CAB-seq software tools

Conventional bisulfite sequencing does not discriminate between different oxidized forms (Huang et al., 2010). Several new methods such as oxBS-seq (Booth et al., 2012), TAB-seq (Schuler and Miller, 2012), fCAB-seq (Song et al., 2013) and CAB-seq…
oxBS-MLE
Desktop

oxBS-MLE oxidative bisulfite Maximum Likelihood Estimate

An efficient method based on binomial modeling of paired bisulfite and…

An efficient method based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that oxBS-MLE outperformed…

G T A T C G C T A
Lux
Desktop

Lux

A generative model to quantify DNA methylation modifications from any…

A generative model to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and…

G T A T C G C T A
qDNAmod
Desktop

qDNAmod

A bioinformatic tool for genome-wide quantitative profiling of intercellular…

A bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid…

G T A T C G C T A
LuxGLM
Desktop

LuxGLM

Allows integrative analysis of different oxi-mC data sets with experimental…

Allows integrative analysis of different oxi-mC data sets with experimental parameters and arbitrary, complex experimental designs. The method is applicable in analysis of genome-wide, reduced…

G T A T C G C T A
MOABS
Desktop

MOABS MOdel based Analysis of Bisulfite Sequencing data

A complete, accurate and efficient solution for analysis of large scale…

A complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing. MOABS seamlessly integrates…

G T A T C G C T A
MLML
Desktop

MLML

A useful tool to simultaneously estimate hydroxymethylation (5hmC) and…

A useful tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments.

G T A T C G C T A
BiQ Analyzer…
Desktop

BiQ Analyzer HiMod

Allows to process an amount of bisulfite, oxidative bisulfite, Tet assisted…

Allows to process an amount of bisulfite, oxidative bisulfite, Tet assisted bisulfite, chemical modification-assisted bisulfite or formyl chemical modification-assisted bisulfite sequencing reads…

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