Methpat 2.0.0 – A program for Summarising CpG Methylation Patterns

Methpat 2.0.0

:: DESCRIPTION

Methpat summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.

::DEVELOPER

Bernie Pope

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • Bismark v0.12.2 and it’s dependencies (bwa v0.7.5a-r405).

:: DOWNLOAD

 Methpat

:: MORE INFORMATION

Citation

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.
Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A.
BMC Bioinformatics. 2016 Feb 24;17(1):98. doi: 10.1186/s12859-016-0950-8.

DeepMethyl 20151121 – Predicting DNA Methylation State of CpG Dinucleotide

DeepMethyl 20151121

:: DESCRIPTION

DeepMethyl is a web server for predicting the DNA Methylation State of CpG Dinucleotide using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns.

::DEVELOPER

Dr. Zheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks.
Wang Y, Liu T, Xu D, Shi H, Zhang C, Mo YY, Wang Z.
Sci Rep. 2016 Jan 22;6:19598. doi: 10.1038/srep19598.

PrEMeR-CG – Probabilistic Extension of Methylated Reads at CpG resolution

PrEMeR-CG

:: DESCRIPTION

PrEMeR-CG is a computational approach that harnesses the implicit information associated with library fragment profiles to infer nucleotide-resolution methylation values in addition to read counts data.

CpG binning quantifies the methylation for each CpG in the genome using aligned reads and a fragment profile.

::DEVELOPER

Ralf Bundschuh’s Statistical Physics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 PrEMeR-CG

:: MORE INFORMATION

Citation

PrEMeR-CG: Inferring Nucleotide Level DNA Methylation Values from MethylCap-Seq Data.
Frankhouser DE, Murphy M, Blachly JS, Park J, Zoller MW, Ganbat JO, Curfman J, Byrd JC, Lin S, Marcucci G, Yan P, Bundschuh R.
Bioinformatics. 2014 Aug 31. pii: btu583.

QUMA 1.1.13 – Visualize and Quantify Bisulfite Sequence data for CpG Methylation Analysis

QUMA 1.1.13

:: DESCRIPTION

QUMA (QUantification tool for Methylation Analysis)is a web-based tool for CpG methylation analysis.Youcan easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis

::DEVELOPER

Laboratory for Mammalian Epigenetic StudiesCenter for Developmental BiologyRIKEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QUMA

:: MORE INFORMATION

Citation

Yuichi Kumaki, Masaaki Oda & Masaki Okano
QUMA: quantification tool for methylation analysis
Nucleic Acids Res. 36, W170-W175 (2008).