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QDMR specifications


Unique identifier OMICS_00623
Alternative name Quantitative Differentially Methylated Region
Software type Application/Script, Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes


Version Operating System DOI Size Download Info
32/64 bits
10.24347/OMIC_623_1.0/wlm8664 21.17 Mo get_app



  • person_outline Hongbo Liu

Additional information

QDMR is embedded in EpiDiff as the second module.

Publication for Quantitative Differentially Methylated Region

QDMR citations


Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues

J Transl Med
PMCID: 5299650
PMID: 28178989
DOI: 10.1186/s12967-017-1122-y

[…] pplied to identify population-level differentially methylated (DM) CpG sites in cancer tissues compared with normal controls using various statistical methods such as the Shannon entropy based method QDMR [], empirical Bayes model DiffVar [] and T test []. However, the inter-individual heterogeneity of DM CpG sites was ignored in these approaches. Thus a novel computational tool is needed to detec […]


Integrating Epigenomics into the Understanding of Biomedical Insight

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

[…] e), 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 with some previous methods and claims best performance, su […]


DNMT3A and TET2 compete and cooperate to repress lineage specific transcription factors in hematopoietic stem cells

Nat Genet
PMCID: 4957136
PMID: 27428748
DOI: 10.1038/ng.3610

[…] ng the four genotypes. Next, the mean methylation levels of CpGs covered with at least 5 reads in DMRs were computed in each genotype. Finally, the DMRs were further assessed by a quantitative method QDMR based on shannon entropy among the four genotypes. The DMRs with default entropy value <2 remained. To study the patterns of dynamic change of DNA methylation and their coordinate regulation rela […]


swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

PLoS One
PMCID: 4503785
PMID: 26176536
DOI: 10.1371/journal.pone.0132866

[…] placement and functional consequences of DNA methylation in cancer[, ].To date, a number of tools have been developed and available for DMRs identification from methylomes. For example, dmrFinder[], QDMR[] and methylMnM[] are designed for the analysis of DMR based on microarray, MeDIP-seq or MRE-seq data. To perform methylome DMR detection at single-base resolution, CpG_MPs[], DSS[], bsseq[], eDM […]


The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer

BMC Genomics
PMCID: 4440512
PMID: 25997618
DOI: 10.1186/s12864-015-1552-y

[…] genomic annotation information was based on the hg19 human genome (http://genome.ucsc.edu). Differentially methylated regions (DMRs) were identified by quantitative differentially methylated regions (QDMR) []. The QDMR is a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles with a concept of ‘DNA methylation entropy’ []. The ‘DNA methyl […]


A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro

BMC Genomics
PMCID: 4008136
PMID: 24106769
DOI: 10.1186/1471-2164-14-692

[…] at allows for an exact Fisher’s test. Also in this case, we consistently assumed as threshold of statistical significance of 5%. Filtering with HBA the CGIs classified as differentially methylated by QDMR reduces on average their number of about 20%. […]


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QDMR institution(s)
College of Bioinformatics Science and Technology, Harbin Institute of Technology, Harbin, China; The Third Affiliated Hospital, Harbin Medical University, Harbin, China; Department of Life Science and Engineering, Harbin Institute of Technology, Harbin, China

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