Tag: DNA Methylation

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.

MethylSig 0.99.4 – Whole Genome DNA Methylation Analysis Pipline

MethylSig 0.99.4

:: 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.

MethylMix 2.20.0 – Identifying DNA Methylation Driven Genes

MethylMix 2.20.0

:: DESCRIPTION

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

::DEVELOPER

 Gevaert lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • R BioConductor / Matlab

:: DOWNLOAD

 MethylMix

:: 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

ADMIRE v1.1.0 – Analysis of DNA Methylation in Genomic Regions

ADMIRE v1.1.0

:: DESCRIPTION

ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K and Infinium MethylationEpic assays.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ADMIRE

:: MORE INFORMATION

Citation:

Preussner J, Bayer J, Kuenne C and Looso M.
ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay.
Epigenetics Chromatin, 8, 51(2015), doi:10.1186/s13072-015-0045-1

BatMeth 1.04b – Improved Mapper for Bisulfite Sequencing Reads on DNA Methylation

BatMeth 1.04b

:: DESCRIPTION

BatMeth is an algorithm that integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes to improve unique mapping rate, speed and precision.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BatMeth

:: MORE INFORMATION

Citation

Genome Biol. 2012 Oct 3;13(10):R82. [Epub ahead of print]
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.

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.

MethMarker 1.0.680 – Facilitate Design of DNA Methylation Assays

MethMarker 1.0.680

:: DESCRIPTION

MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.

::DEVELOPER

Peter Schüffler, Christoph Bock, Thomas Mikeska and Thomas Lengauer , Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 MethMarker

:: MORE INFORMATION

Citation:

MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock
Genome Biology 2009, 10:R105doi:10.1186/gb-2009-10-10-r105