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NHMMfdr specifications


Unique identifier OMICS_18711
Name NHMMfdr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.6
Stability Stable
MASS, locfdr
Maintained Yes



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  • person_outline Pei Fen Kuan <>

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Publication for NHMMfdr

NHMMfdr in publications

PMCID: 5817089
PMID: 29491831
DOI: 10.3389/fnmol.2018.00039

[…] for the remaining cpgs (5 mc: n = 142,304; 5 hmc: n = 140,664), p-values were transformed to z-scores. a hidden markov model was used to adjust for local index of significance (alis) using r package nhmmfdr (kuan and chiang, ) with all parameters set to default with the exception of: model type set to hmm, alternative hypothesis type set to “kernel,” null hypothesis type set to empirical null […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] (bumphunting), tunable kernel smoothing (dmr-cate), nonparametric and kernel-based method (m3d), beta-binomial model (methylsig), beta-binomial hierarchical model (moabs), hidden markov model (nhmmfdr), three-state hmm (methpipe), shannon entropy (qdmr), and a binary segmentation algorithm combined with a two-dimensional statistical test (metilene). usually, the latest software compares […]

NHMMfdr institution(s)
Department of Biostatistics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
NHMMfdr funding source(s)
Supported in part by NCI grants 5-P30-CA16086-34, 1R21CA134368-01A1, P05CA106991, Susan G. Komen Foundation grant KG081397, Alfred P. Sloan Fellowship (D.C.) and University Cancer Research Fund.

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