Tag: Methylated Region

ICDMR – Identification of Consistently Differentially Methylated Regions

ICDMR

:: DESCRIPTION

ICDMR is an unsupervised approach, where there is no need to choose the comparative group in advance, and is able to identify methylation modifications either among individuals or between potential subgroups in a population.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 ICDMR

:: MORE INFORMATION

Citation

A novel method for identification and quantification of consistently differentially methylated regions.
Hsiao CL, Hsieh AR, Lian IeB, Lin YC, Wang HM, Fann CS.
PLoS One. 2014 May 12;9(5):e97513. doi: 10.1371/journal.pone.0097513

MRmediation 1.0.1 – Causal Mediation Method with Methylated Region (MR) as the Mediator

MRmediation 1.0.1

:: DESCRIPTION

MRmediation is a causal mediation approach under the counterfactual framework to test the significance of total, direct and indirect effects.

::DEVELOPER

Qi Yan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

MRmediation

:: MORE INFORMATION

Citation

Yan Q, Forno E, Celedón JC, Chen W.
A region-based method for causal mediation analysis of DNA methylation data.
Epigenetics. 2021 Mar 23:1-11. doi: 10.1080/15592294.2021.1900026. Epub ahead of print. PMID: 33757385.

Bisulfighter 20150318 – accurate Detection of Methylated Cytosines and differentially Methylated Regions

Bisulfighter 20150318

:: DESCRIPTION

Bisulfighter is a software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data. Compared with other published tools, Bisulfighter provides greater sensitivity for mCs with fewer false positives, more precise estimates of mC levels, more exact locations of DMRs, and better agreement of DMRs with differentially expressed genes. The superior accuracy is maintained under various sequencing depths and tissue types.

::DEVELOPER

Bisulfighter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • ComMet
  • Boost C++ library

:: DOWNLOAD

 Bisulfighter

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Apr 1;42(6):e45. doi: 10.1093/nar/gkt1373. Epub 2014 Jan 13.
Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions.
Saito Y1, Tsuji J, Mituyama T.

DiMmer – Detection of differentially Methylated Regions

DiMmer

:: DESCRIPTION

DiMmer is an open source software package identifying differentially methylated regions in the human genome.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

DiMmer

:: MORE INFORMATION

Citation

DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data.
Methods Mol Biol. 2018;1807:51-62. doi: 10.1007/978-1-4939-8561-6_5.
Frisch T, Gøttcke J, Röttger R, Tan Q, Baumbach J.

MethylAction – Detecting Differentially Methylated Regions (DMRs) that distinguish Biological and Disease subtypes

MethylAction

:: DESCRIPTION

MethylAction is an R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide.

::DEVELOPER

Jeff Bhasin,  in the Ting Lab at the Cleveland Clinic Genomic Medicine Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 MethylAction

:: MORE INFORMATION

Citation

MethylAction: detecting differentially methylated regions that distinguish biological subtypes.
Bhasin JM, Hu B, Ting AH.
Nucleic Acids Res. 2016 Jan 8;44(1):106-16. doi: 10.1093/nar/gkv1461.