RLM – Read level DNA methylation analysis of Bisulfite Converted Sequencing data

RLM

:: DESCRIPTION

RLM is a fast and scalable tool for the computation of frequently used Read-Level Methylation statistics.

::DEVELOPER

RLM Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

RLM

:: MORE INFORMATION

Citation

Hetzel S, Giesselmann P, Reinert K, Meissner A, Kretzmer H.
RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data.
Bioinformatics. 2021 Oct 2:btab663. doi: 10.1093/bioinformatics/btab663. Epub ahead of print. PMID: 34601556.

iDNA-ABT – Detecting DNA Methylation with Adaptive Features and Transductive Information Maximization

iDNA-ABT

:: DESCRIPTION

iDNA-ABT is an advanced deep learning model that utilizes adaptive embedding based on bidirectional transformers for language understanding (BERT) together with a novel transductive information maximization (TIM) loss.

::DEVELOPER

iDNA-ABT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

iDNA-ABT

:: MORE INFORMATION

Citation

Yu Y, He W, Jin J, Cui L, Zeng R, Wei L.
iDNA-ABT : advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.
Bioinformatics. 2021 Oct 2:btab677. doi: 10.1093/bioinformatics/btab677. Epub ahead of print. PMID: 34601568.

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.

MethLAB 2.1 – Analysis of DNA Methylation Microarray data

MethLAB 2.1

:: 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

Lab of Alicia Smith, PhD, 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

BEclear 2.8.0 – Batch Effect Detection and Adjustment in DNA Methylation Data

BEclear 2.8.0

:: DESCRIPTION

BEclear enables researchers to identify those portions of the data that deviate statistically significant from the remaining data and to replace these portions by typical values reconstructed from neighboring data entries based on latent factor models.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

BEclear

:: MORE INFORMATION

Citation

Akulenko R, Merl M, Helms V.
BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.
PLoS One. 2016 Aug 25;11(8):e0159921. doi: 10.1371/journal.pone.0159921. PMID: 27559732; PMCID: PMC4999208.

RnBeads 2.10.0 – Comprehensive DNA Methylation Analysis

RnBeads 2.10.0

:: 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.

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.

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

Z. WANG LAB

:: 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.

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.

DeepMod v0.1.3 – Deep-learning tool for DNA Methylation Detection on Nanopore data

DeepMod v0.1.3

:: DESCRIPTION

DeepMod is a computational tool which takes long-read signals as input and outputs modification summary for each genomic position in a reference genome together with modification prediction for each base in a long read.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepMod

:: MORE INFORMATION

Citation

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K.
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Nat Commun. 2019 Jun 4;10(1):2449. doi: 10.1038/s41467-019-10168-2. PMID: 31164644; PMCID: PMC6547721.