NHMMfdr statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool NHMMfdr

Tool usage distribution map

info info

Associated diseases


Popular tool citations

chevron_left Differentially methylated region detection chevron_right
Want to access the full stats & trends on this tool?

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




No version available


  • person_outline Pei Fen Kuan

Additional information


Publication for NHMMfdr

NHMMfdr citations


Species Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution

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 wit […]


Integrating Epigenomics into the Understanding of Biomedical Insight

Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] ection (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 wit […]

Want to access the full list of citations?
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.

NHMMfdr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NHMMfdr