Bisulfighter statistics

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chevron_left Methylation scoring Differentially methylated region detection chevron_right
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Bisulfighter specifications

Information


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 in publications

 (5)
PMCID: 4682380
PMID: 26681544
DOI: 10.1186/1471-2164-16-S12-S3

[…] exact test and methylation level smoothing., our method enables accurate dmr detection from bisulfite-seq data. the implementation of our method is named commet, and distributed as a part of bisulfighter package, which is available at http://epigenome.cbrc.jp/bisulfighter., cytosine methylation is an epigenetic modification that affects many biological processes including normal […]

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

[…] 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 […]

PMCID: 4666378
PMID: 26184873
DOI: 10.1093/nar/gkv715

[…] 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 […]

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

[…] 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., […]

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

[…] 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 […]


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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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