bsseq specifications

Information


Unique identifier OMICS_00581
Name bsseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14
Stability Stable
Requirements methods, BiocGenerics, GenomicRanges, SummarizedExperiment, parallel
Maintained Yes

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Documentation


Maintainers


  • person_outline Kasper Daniel Hansen <>
  • person_outline Rafael A. Irizarry <>
  • person_outline Benjamin Langmead <>

bsseq article

bsseq citations

 (2)
2017
PMCID: 5634322

[…] of freely available bisulfite-converted sequence aligners. in this study we used the bismark methylation aligner10, however, we expect that similar alignment results can be achieved using the bsmooth pipeline11. alignment of the fastq data in the form of bam files can be viewed using popular genome browsers such as the ucsc genome browser12, the ensembl browser13, or the broad institute‚Äôs […]

2016
PMCID: 4926291

[…] only sites covered by all samples are comparable. to enable the comparison, the comparing statistics such as methylation difference, t-score from t test or p value is needed in the testing. in the bsmooth software, a beta-binomial is assumed to be the suitable model for replicated bisulfite sequencing data. the observation is assumed to be binomially distributed, whereas the methylated […]

bsseq institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
bsseq funding source(s)
Partially supported by HG004059 and P50HG003233.

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