MethPipe 3.4.3 – DNA Methylation Data Analysis Pipeline

MethPipe 3.4.3

:: DESCRIPTION

The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS).

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MethPipe

:: MORE INFORMATION

Citation

Song Qiang, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD.
A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics.
PloS one 8.12 (2013): e81148.

MethylMix 1.6.0 – Identifying DNA Methylation Driven Genes

MethylMix 1.6.0

:: DESCRIPTION

MethylMix is an algorithm implemented in R to identify disease specific hyper and hypomethylated genes.

::DEVELOPER

Olivier Gevaert <olivier.gevaert at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • R BioConductor / Matlab

:: DOWNLOAD

 MethylMix , for Matlab

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 20. pii: btv020. [Epub ahead of print]
MethylMix: an R package for identifying DNA methylation driven genes.
Gevaert O

MethylSig 0.4.3 – Whole Genome DNA Methylation Analysis Pipline

MethylSig 0.4.3

:: DESCRIPTION

MethylSig is our new R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments. Methylsig tests for differentially methylated sites (DMCs) or regions (DMRs) using a beta-binomial model to account for the coverage and variation among samples at each CpG site or region, and has a well-calibrated Type 1 error rate. Several options exist for either site-specific or sliding window tests, combining strands, filtering sites, and for local variance estimation. In addition, methylSig offers numerous functions for annotating and visualizing results, and testing for enrichment of overlap with the binding sites of transcription factors.

::DEVELOPER

The Sartor Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MethylSig

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 16. pii: btu339. [Epub ahead of print]
methylSig: a whole genome DNA methylation analysis pipeline.
Park Y1, Figueroa ME1, Rozek LS2, Sartor MA3.

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.

BiQ Analyzer 3.0 / BiQAnalyzer HT / BiQ Analyzer HiMod – Tool for DNA Methylation Analysis

BiQ Analyzer 3.0 /  BiQAnalyzer HT / BiQ Analyzer HiMod

:: DESCRIPTION

BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing.

 BiQAnalyzer HT is the major upgrade of the popular BiQAnalyzer tool specifically designed to aid the analysis of high-throughput bisulfite amplicon sequencing data.

BiQ Analyzer HiMod is the major upgrade of the popular BiQAnalyzer HT tool specifically designed to aid the analysis of high-throughput bisulfite amplicon sequencing data.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

BiQ Analyzer ,BiQ Analyzer HT ,

:: MORE INFORMATION

Citation

Bock, C., S. Reither, T. Mikeska, M. Paulsen, J. Walter and T. Lengauer (2005).
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.”
Bioinformatics 21(21): 4067-8.

Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter and Christoph Bock
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.
Nucl. Acids Res. (2011) 39 (suppl 2): W551-W556.

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.
Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W501-7. doi: 10.1093/nar/gku457.

RnBeads 0.99.19 – Comprehensive DNA Methylation Analysis

RnBeads 0.99.19

:: DESCRIPTION

RnBeads is the first software tool that implements a comprehensive workflow for analyzing DNA methylation data in the context of large cohort studies. Its functionality comprises data normalization, quality control, probe and sample filtering, handing of batch effects, global DNA methylation analysis, detection of differentially methylated regions and interpretation by statistical enrichment analysis.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 RnBeads

:: MORE INFORMATION

Citation

Comprehensive analysis of DNA methylation data with RnBeads.
Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C.
Nat Methods. 2014 Sep 28. doi: 10.1038/nmeth.3115.

MethLAB 1.5 – Analysis of DNA Methylation Microarray data

MethLAB 1.5

:: DESCRIPTION

MethLAB provides a graphical user interface (GUI) to facilitate analysis of DNA methylation microarray data, allowing users with no experience using statistical software to implement flexible and powerful analyses of array-based DNA methylation data.

::DEVELOPER

Department of Human Genetics, Emory University School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

MethLAB

:: MORE INFORMATION

Citation

Varun Kilaru, Richard T. Barfield, James W. Schroeder, Alicia K. Smith, Karen N. Conneely.
MethLAB: A GUIpackage for the analysis of array-based DNA methylation data (2012).
Epigenetics, Volume 7, Issue 3

FadE 0.0.2 – DNA Methylation Detection

FadE 0.0.2

:: DESCRIPTION

FadE is a software package which was designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 FadE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan 7;41(1):e14. doi: 10.1093/nar/gks830. Epub 2012 Sep 10.
FadE: whole genome methylation analysis for multiple sequencing platforms.
Souaiaia T1, Zhang Z, Chen T.

DMEAS 2012 – DNA Methylation Entropy Analysis Software

DMEAS 2012

:: DESCRIPTION

DMEAS is a user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

::DEVELOPER

DMEAS team

:: SCREENSHOTS

DMEAS

:: REQUIREMENTS

  • Windows
  • .net framework 4.0 environments

:: DOWNLOAD

 DMEAS

:: MORE INFORMATION

Citation

DMEAS: DNA methylation entropy analysis software.
He J, Sun X, Shao X, Liang L, Xie H.
Bioinformatics. 2013 Aug 15;29(16):2044-5. doi: 10.1093/bioinformatics/btt332.

methylSpectrum v2 – DNA Methylation as a Surrogate for Cell Mixture

methylSpectrum v2

:: DESCRIPTION

methylSpectrum is a software for deconvolution of DNA methylation array data into source contributions from distinct cell types. The major application of this software is to determine the composition of white blood cells (WBCs) from DNA methylation array data assayed in whole blood

::DEVELOPER

E. Andres Houseman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R package

:: DOWNLOAD

 methylSpectrum

:: MORE INFORMATION

Citation

DNA methylation arrays as surrogate measures of cell mixture distribution.
Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT.
BMC Bioinformatics. 2012 May 8;13:86. doi: 10.1186/1471-2105-13-86.