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BioHMM specifications

Information


Unique identifier OMICS_08930
Name BioHMM
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
Stability Stable
Maintained No

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Publication for BioHMM

BioHMM in publications

 (10)
PMCID: 4468211
PMID: 26076459
DOI: 10.1371/journal.pone.0129280

[…] to zero across the entire genome. direct visualization was used to assess structural variations across the genome. finally, segmentation was performed by a heterogeneous hidden markov model, termed biohmm [], which was adapted for ngs data., to calculate gene-level cnv in the 07–0120 tumor tissue cohort, we used the depth of gene exon-specific sequenced reads with 1-bp resolution. we estimated […]

PMCID: 3449101
PMID: 23008709
DOI: 10.1155/2012/876976

[…] the package dnacopy [, ], an adaptive weights smoothing method from the package glad [], an homogeneous hidden markov model (homhmm) provided by the package acgh [], and a biologically tuned hmm (biohmm) from the package snapcgh []. by consolidating data from the four analyses, we identified the most robust cna regions of interest in the dataset. based on our comparison of methods […]

PMCID: 3205051
PMID: 22073121
DOI: 10.1371/journal.pone.0026975

[…] 22,600,400, and 13 samples participate strongly in this cnvz., we compared mgvd with the seven algorithms implemented in cghweb , namely cbs , faseg , cghflasso , cghseg , quantreg , glad , and biohmm . we ran these algorithms on chromosome 22 only, as this is the smallest chromosome, because all seven algorithms terminated after several days when run on data from all chromosomes. […]

PMCID: 3011854
PMID: 21083884
DOI: 10.1186/1471-2164-11-639

[…] from the averaged ~6 kb. pointwise averaging of all computed profiles and maps of gains/losses for smoothed/segmented obtained from several algorithms (lowess, wavelet, quantreg, ruavg, cbs, cghseg, biohmm, cghflasso, glad, and faseg) and summary data were generated. pointwise averaging was shown to have good performances in calling alteration of copy number [] and was chosen to compensate […]

PMCID: 2728899
PMID: 19696946
DOI: 10.1155/2009/201325

[…] [, ]. a method based on hierarchical clustering along chromosomes is used in the clac package []. hidden markov models, where copy numbers are hidden states, are used in the acgh package [], and biohmm extends the algorithm of fridlyand et al. by taking the distance between clones and other variables into account []. , cghmcr helps to locate minimum common regions (mcrs) altered across […]


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BioHMM institution(s)
Hutchison-MRC Research Centre, Department of Oncology, Computational Biology Group, University of Cambridge Hills Road, Cambridge; Department of Applied Mathematics and Theoretical Physics, University of Cambridge Wilberforce Road, Cambridge

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