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BiSeq specifications

Information


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
Requirements
methods, parallel, BiocGenerics, Biobase, IRanges, GenomicRanges, R(>=2.15.2), rtracklayer, IRanges(>=1.17.24), Formula, betareg, lokern
Maintained Yes

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Documentation


Publication for BiSeq

BiSeq in pipelines

 (2)
2017
PMCID: 5459992
PMID: 28556835
DOI: 10.1038/ncomms15527

[…] specified. bowtie short read aligner was used. the bisulfite conversion rate was estimated by calculating the c to t conversion at non-cpg sites. differential methylation region was calculated with biseq. dmrs were considered significant with p<0.05. rgadem was used for unseeded motif analysis with default settings and motiv for e value calculation and visualization based on jaspar 2010 […]

2016
PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] comparing 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 [] (e.g., biseq takes spatial correlation into account in dmr prediction []). weak dna methylation differences can be better measured by estimating the standard deviation from biological replicates to obtain […]


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BiSeq in publications

 (17)
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] to statistically determine methylation differences at individual cpg sites. one such recent method, known as dss [, ], has been compared to several methods (such as methylkit [], bsmooth [], biseq [], radmeth [], and moabs []), using simulated as well as real data and has been found to be more preferable than these methods. moreover, metilene, a recently proposed dmr finder [], was found […]

PMCID: 5785820
PMID: 29416570
DOI: 10.1186/s13148-018-0446-7

[…] reads were done with trim galore v0.4.0 & cutadapt v1.8.3 using the --rrbs flag. bismark v0.14.4 [] was used for aligning the reads to the hg19 genome and for computing the cpg coverage. the biseq package v1.10 [] calculated methylation levels and found dmrs. standard settings were used, except for the function: “clustersites”, where the settings perc.samples = 0.5 and min.sites = 5 […]

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

[…] better 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 […]

PMCID: 5680174
PMID: 29123172
DOI: 10.1038/s41598-017-15420-7

[…] galore v0.3.7 and cutadapt v1.4.2. processed reads were mapped to hg38 followed by derivation of cpg methylation using bismark. differentially methylated regions (fdr < 0.1) were identified using biseq from the subset of cpg sites that are covered by at least half of the samples using the following models y~timepoint + subject for each of the hfd-ex and hfd-sed groups. our confidence […]

PMCID: 5514474
PMID: 28716111
DOI: 10.1186/s12885-017-3482-3

[…] software (life technologies). the percent methylation in each cpg was calculated by (number of reads with methylated c/total reads) × 100. the methylation data can be viewed in the igv using the biseq package in r/bioconductor., to compare the bas and bgs methods, sodium bisulfite–modified dna was subjected to pcr with bisulfite sequencing primers for itga4 and znf549, shown in table , […]


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

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