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QDMR specifications

Information


Unique identifier OMICS_00623
Name QDMR
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
Requirements
EpiDiff
Maintained Yes

Versioning


Version Operating System DOI Size Download Info
1.0
32/64 bits
10.24347/OMIC_623_1.0/wlm8664 21.17 Mo get_app

Documentation


Maintainer


  • person_outline Hongbo Liu

Additional information


QDMR is embedded in EpiDiff as the second module.

Publication for Quantitative Differentially Methylated Region

QDMR citations

 (6)
library_books

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

2017
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 […]

library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
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 […]

library_books

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

2016
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 […]

library_books

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

2015
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 […]

library_books

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

2015
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 […]

library_books

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

2013
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%. […]

Citations

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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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