Segway protocols

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Segway specifications

Information


Unique identifier OMICS_06227
Name Segway
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Segway <>
  • person_outline Michael Hoffman <>

Publications for Segway

Segway in pipeline

2017
PMCID: 5529029
PMID: 28700586
DOI: 10.1371/journal.pgen.1006883

[…] repbase update (1.1.3 release) in repbase (http://www.girinst.org/server/repbase/). dhs datasets were obtained from encode (). genome segmentations in six cell types (combined between chromhmm and segway) [–] were obtained from encode (). datasets of cold spring harbor laboratory (cshl) longpolya rna-seq were obtained from encode in the gtf format (). ontology file (go-basic.obo, date; […]


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Segway in publications

 (37)
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] implement ep2vec can be downloaded from https://github.com/wanwenzeng/ep2vec., the majority of our datasets were adapted from targetfinder. promoter and enhancer regions were identified using encode segway [] and chromhmm [] annotations for k562, gm12878, hela-s3, and huvec cell lines, and using roadmap [] epigenomics chromhmm annotations for nhek and imr90 cell lines. since epis could […]

PMCID: 5704084
PMID: 29180482
DOI: 10.14814/phy2.13510

[…] data for hg19 is based on 25 different chromatin states (including eight different chromatin marks, rna polymerase ii, and ctcf binding) that are used to segment the genome using both chromhmm and segway (encode project consortium , hoffman et al. )., subject characteristics are displayed in table  (pescatello et al. ). subjects (n = 23) were middle‐aged, obese caucasian (39%) and af (61%) men […]

PMCID: 5704366
PMID: 29179726
DOI: 10.1186/s12977-017-0378-x

[…] used to analyze the representation of iss in histone mark distributions [] and in chromatin state segment datasets making use of a consensus merge of the segmentations produced by the chromhmm and segway software []. we applied the wilcoxon test on the row-sums of the score matrixes generated from nucleosome occupancy datasets to check for any statistical difference between the conditions. […]

PMCID: 5704019
PMID: 29180722
DOI: 10.1038/s41598-017-16550-8

[…] briefly, the annotations include annotations for refseq, digital genomic footprint and transcription factor binding sites from encode, combined chromhmm and segway annotations for six cell lines, processed dhs data from encode and roadmap epigenomics data and cell type specific h3k4me1, h3k4me3 and h3k9ac data from roadmap epigenomics, h3k27ac […]

PMCID: 5657043
PMID: 29072144
DOI: 10.1186/s12859-017-1828-0

[…] modifications to predict p300 binding sites in human lung fibroblasts and embryonic stem cells []. two research groups have employed unsupervised approaches based on dynamic bayesian networks (segway) [] and hidden markov models (chromhmm) []with signatures in encode data to segment the human genome into regions and then assigned potential functions to these regions. however, […]


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Segway institution(s)
Princess Margaret Cancer Centre, Toronto, ON, Canada; Engineering Physics Program, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Segway funding source(s)
Supported by the Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-03948), the Canadian Institutes of Health Research (384410) and the National Institutes of Health (U41HG007000).

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