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segmentSeq specifications


Unique identifier OMICS_09059
Name segmentSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.14.0
Stability Stable
methods, stats, parallel, graphics, BiocGenerics, IRanges, GenomicRanges, Rsamtools, utils, S4Vectors, GenomeInfoDb, ShortRead, BiocStyle, grDevices, R(>=3.0.0), abind, baySeq(>=2.9.0)
Maintained Yes


No version available



  • person_outline Thomas J. Hardcastle

Publications for segmentSeq

segmentSeq citations


Considerations and complications of mapping small RNA high throughput data to transposable elements

PMCID: 5311732
PMID: 28228849
DOI: 10.1186/s13100-017-0086-z

[…] multiple mapping without any kind of normalization for the number of mapping locations [], the siloco tool of the uea srna toolkit weights each read by its repetitiveness in the genome [], the segmentseq package of bioconductor allocates each m_srna only once to a predefined locus even if it maps to more than one place within this locus or indeed across the genome [], novoalign […]


DNA Methylation Signatures of the Plant Chromomethyltransferases

PLoS Genet
PMCID: 5221884
PMID: 27997534
DOI: 10.1371/journal.pgen.1006526

[…] in trinucleotide context calculated in 500 kb (for a. thaliana) or 1 mb bins (non-weighted mc/(mc+c)). average profiles over genes and transposons were calculated from the cytosine reports with segmentseq v2.4.0 [], using the tair10, itag2.4, agp v3.31, 9311-glean-gene gene annotations, and tair10, tomato ltr transposons [], agp v3.31 (repeat regions larger than 1 kb), 9311-repeat-repbase […]

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segmentSeq institution(s)
Department of Plant Sciences, University of Cambridge, Cambridge, UK

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