BiSeq protocols

BiSeq computational protocol

BiSeq specifications


Unique identifier OMICS_00620
Name BiSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.0.3
Stability Stable
methods, parallel, BiocGenerics, Biobase, IRanges, GenomicRanges, R(>=2.15.2), rtracklayer, IRanges(>=1.17.24), Formula, betareg, lokern
Maintained Yes


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Publication for BiSeq

BiSeq IN pipelines

PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] methylomes with weak differences, extending the testing scale from one c to a cluster of neighboring cs can reduce the number of hypothesis tests to improve the statistical power [91] (e.g., biseq takes spatial correlation into account in dmr prediction [115]). weak dna methylation differences can be better measured by estimating the standard deviation from biological replicates […]

PMCID: 4790440
PMID: 26366945
DOI: 10.2217/epi.15.21

[…] and identify dmrs. by smoothing the procedure reduces outliers from cpgs with low coverage. dmrs are identified by grouping cpgs with t statistics above thresholds and with minimum number of cpgs. biseq [67] is mainly for targeted bisulfite sequencing such as rrbs. it starts with defining cpg clusters by finding cpg sites that are frequently covered across samples (e.g., >20 cpgs and apart […]

BiSeq institution(s)
Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus, Münster, Germany

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