Bisulfighter statistics

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Citations per year

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

This map represents all the scientific publications referring to Bisulfighter per scientific context
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Popular tool citations

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Bisulfighter specifications

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Unique identifier OMICS_00593
Name Bisulfighter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Bisulfighter

Bisulfighter citations

 (6)
library_books

Detection of differentially methylated regions from bisulfite seq data by hidden Markov models incorporating genome wide methylation level distributions

2015
BMC Genomics
PMCID: 4682380
PMID: 26681544
DOI: 10.1186/1471-2164-16-S12-S3

[…] tion. Furthermore, our HMM-based method achieves better accuracy than other methods using Fisher's exact test and methylation level smoothing. The implementation of ComMet is distributed as a part of Bisulfighter package, which is available at http://epigenome.cbrc.jp/bisulfighter. […]

library_books

GIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history

2015
BMC Genomics
PMCID: 4682400
PMID: 26679412
DOI: 10.1186/1471-2164-16-S12-I1

[…] curacy and sensitivity of methylation detection. Differentially methylated regions (DMR) may represent known transcription factor binding sites or new candidate regulatory elements. The developers of Bisulfighter [] improved the DMR detection capability from bisulfite sequencing data by replacing empirical parameters with emission functions for HMM-based DMR detection [] Complimentary to the afore […]

library_books

Detection of differentially methylated regions from whole genome bisulfite sequencing data without replicates

2015
Nucleic Acids Res
PMCID: 4666378
PMID: 26184873
DOI: 10.1093/nar/gkv715

[…] al conditions. A number of statistical methods and computational tools have been developed recently, including BSmooth (), MethylKit (), GBSA (), BiSeq (), DSS (), MOABS (), DMAP (), MethylSig () and Bisulfighter ().Similar to other sequencing experiments, the raw data from WGBS experiments are short sequence reads. After alignment and data processing, the data can be summarized as a pair of count […]

library_books

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

2015
PLoS One
PMCID: 4503785
PMID: 26176536
DOI: 10.1371/journal.pone.0132866

[…] sequencing data, may not make a good performance for WGBS; while CpG_MPs, which combined hotspot algorithm and entropy, can be applied to DMR detection without replicates. ComMet, a tool packaged in Bisulfighter[], employed HMM model to detect DMR without replicates. Finally, to confirm the practical utility of swDMR to samples without replicates, CpG_MPs and ComMet were implemented to do the com […]

library_books

Methylome, transcriptome, and PPARγ cistrome analyses reveal two epigenetic transitions in fat cells

2014
Epigenetics
PMCID: 4169011
PMID: 25093444
DOI: 10.4161/epi.29856

[…] ne expression was evaluated according to the fold change in FPKM. Activated and repressed genes were determined according to the threshold of a 2-fold FPKM change.MethylC-Seq reads were mapped by the Bisulfighter program, which has been recently confirmed to be accurate for bisulfite-converted DNA alignment. For each CpG in the reference, methylation was measured by the mC value, i.e., the fractio […]

library_books

Using beta binomial regression for high precision differential methylation analysis in multifactor whole genome bisulfite sequencing experiments

2014
BMC Bioinformatics
PMCID: 4230021
PMID: 24962134
DOI: 10.1186/1471-2105-15-215

[…] for comparing epigenomes of a pair of samples is Fisher’s Exact Test [-]. There are also DM detection algorithms based on hidden Markov models (HMMs). A recently released tool ComMet, included in the Bisulfighter methylation analysis suite [], is also designed to detect DM regions and DM sites between two samples. Another HMM-based DM detection method is included in the MethPipe methylation analys […]


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Bisulfighter institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan; Japan Science and Technology Agency, CREST, Kawaguchi, Japan; Program in Bioinformatics and Integrative Biology,University of Massachusetts Medical School, Worcester, MA, USA

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