[HTML][HTML] DMRforPairs: identifying differentially methylated regions between unique samples using array based methylation profiles

MA Rijlaarsdam, YG van der Zwan, LCJ Dorssers… - BMC …, 2014 - Springer
… However, when analyzing small numbers of samples with unique characteristics (eg normal
and affected tissue of a clinically unique patient or a manipulated cell model), large series of …

[HTML][HTML] De novo identification of differentially methylated regions in the human genome

TJ Peters, MJ Buckley, AL Statham, R Pidsley… - Epigenetics & …, 2015 - Springer
… the effect size is very small – such as, for example, where no differential probes with P<0.05 …
, gene associations and number of constituent CpGs per region are also reported. The user …

Dmrff: Identifying differentially methylated regions efficiently with power and control

M Suderman, JR Staley, R French, R Arathimos… - BioRxiv, 2018 - biorxiv.org
… Each targeted region typically includes a small number of … , ie small numbers of samples
relative to the number of … threshold, 0.05 divided by the number of CpG sites tested. This …

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays

S Mallik, GJ Odom, Z Gao, L Gomez… - Briefings in …, 2019 - academic.oup.com
number of software tools have been developed for identifying disease-associated differentially
methylated regions (… Differential methylation of a small subset (ie 500) of the clusters were …

Methods for identifying differentially methylated regions for sequence-and array-based data

DP Chen, YC Lin, CSJ Fann - Briefings in functional genomics, 2016 - academic.oup.com
… However, Bump Hunting is not sensitive to finding small DMRs involving a small number
of loci [46]. Similar to ICDMR, one of the previously mentioned methods, WFMM [36] also …

Epigenetics: the DNA methylation profile of tissue-dependent and differentially methylated regions in cells

J Ohgane, S Yagi, K Shiota - Placenta, 2008 - Elsevier
… a small number of aberrant DNA methylation profiles, ie 1–2% of RLGS spots [51]. Thus,
the DNA methylation … is a slightly aberrant DNA methylation status in a small number of T-DMRs. …

DMAP: differential methylation analysis package for RRBS and WGBS data

PA Stockwell, A Chatterjee, EJ Rodger… - …, 2014 - academic.oup.com
… to the differentially methylated regions in a format that is easily analyzed with limited … A
DMC approach is perhaps more useful when a small number of CpG sites are analyzed. …

mCSEA: detecting subtle differentially methylated regions

J Martorell-Marugán, V González-Rumayor… - …, 2019 - academic.oup.com
… 0.2 and it outperformed the rest of methods when the methylation differences were especially
small (0.05). In addition, mCSEA returns a low number of FP, resulting in a high PPV for all …

[HTML][HTML] DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data

JM Gaspar, RP Hart - BMC bioinformatics, 2017 - Springer
… 2c), thus indicating that this genomic region has a low level of methylation. On the other … )
due to their smaller size (Fig. 4). The overall large quantity of differential methylation found by …

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions

Y Saito, J Tsuji, T Mituyama - Nucleic acids research, 2014 - academic.oup.com
… compared at the same number of false-positive mC calls (Figure 2a). The difference in
true-positive rates was especially remarkable when only a small number of false positives were …