MOABS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MOABS
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Tool usage distribution map

This map represents all the scientific publications referring to MOABS per scientific context
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Protocols

MOABS specifications

Information


Unique identifier OMICS_04480
Name MOABS
Alternative name MOdel based Analysis of Bisulfite Sequencing data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for MOdel based Analysis of Bisulfite Sequencing data

MOABS citations

 (21)
call_split

Genome wide tracking of dCas9 methyltransferase footprints

2018
Nat Commun
PMCID: 5807365
PMID: 29426832
DOI: 10.1038/s41467-017-02708-5
call_split See protocol

[…] S raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap. DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package. CpA calling was performed using mcall with setting adjusted to detect CpAs. […]

library_books

Genome wide DNA methylation analysis reveals that mouse chemical iPSCs have closer epigenetic features to mESCs than OSKM integrated iPSCs

2018
PMCID: 5833453
PMID: 29416007
DOI: 10.1038/s41419-017-0234-x

[…] 0-bp reads.Sequencing reads of RRBS were aligned to mouse reference genome (mm10) using BSMAP v2.90 with up to 8% mismatches. Only uniquely mapped pairs were retained for analysis of DNA methylation. MOABS v1.3.2 was used to merge replicates and measure CpG methylation levels. Only the CpGs with ≥10-fold coverage in all samples were kept for differentially methylated CpG sites (DMCs) and DMR calli […]

library_books

Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain

2018
mSystems
PMCID: 5801341
PMID: 29435496
DOI: 10.1128/mSystems.00219-17

[…] Raw sequencing reads were trimmed by 10 bp at each end and aligned to the human genome build hg19/GRCh37 using BSMAP (). Methylation levels at CpGs were determined with the mCall package from MOABS (). Only CpGs covered by 5 or more reads were used for analysis. DMRs were identified by a two-sample weighted t test, and multiple-testing correction was performed with the R q value package. F […]

library_books

Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC

2018
Nucleic Acids Res
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] 2.89) () with paired mode and two allowable mismatches. In total, we identified 14.6 million CpG sites with coverage ≥10 reads and our downstream bioinformatic analyses were based on these CpG sites. MOABS () and BSeQC () were used to do the quality control and to calculate the methylation ratio for each CpG site. We defined DMRs as the regions between two samples that have an absolute difference […]

library_books

Base Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells

2018
PMCID: 5844302
PMID: 29326230
DOI: 10.1534/g3.117.300446

[…] lation alterations in splenic naïve B cells. To define regions that are differentially methylated between Dnmt3a+/+ and Dnmt3a−/− B cells, we utilized the differential methylation analysis algorithm, MOABS (Model-based Analysis of Bisulfite Sequencing data) (). In total, 449 DMRs were identified, and both hypomethylated DMRs (Table S2 in File S1) and hypermethylated DMRs (Table S3 in File S1) were […]

library_books

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

2017
F1000Res
PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] tter variance modelling. For example, DSS fits a Bayesian hierarchical beta-binomial model to BS-seq data and uses Wald tests to detect DMRs . Other software using beta-binomial model include BiSeq , MOABS and RADMeth .In this workflow, we demonstrate an edgeR approach of differential methylation analysis. edgeR is one of the most popular Bioconductor packages for assessing differential expressio […]


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