MeDIP-seq data analysis bioinformatics software tools

MeDIP is a technology capable of targeting the vast majority of the methylome. It involves antibodies directed against mC or mCG to precipitate methylated DNA fragments. MeDIP is able to detect methylated cytosines in both mC and mCG contexts.

Desktop app
RnBeads RnBeads

RnBeads

An R package for comprehensive analysis of DNA methylation data obtained with…

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite…

Desktop app
G T A T C G C T A Modeling Experimental… Modeling Experimental Data with MeDIP Enrichment

MEDME Modeling Experimental Data with MeDIP Enrichment

Allows the prediction of absolute and relative methylation levels based on…

Allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments. MEDME is an experimental and analytical methodology designed to obtain…

Desktop app
G T A T C G C T A MEDIPS MEDIPS

MEDIPS

Provides functions for the quality control and analysis of data derived from…

Provides functions for the quality control and analysis of data derived from immunoprecipitation (IP)-seq samples. MEDIPS starts with the aligned reads (typically bam files) and can be used for any…

Desktop app
G T A T C G C T A Repitools Repitools

Repitools

A software package for the analysis of enrichment-based epigenomic data.…

A software package for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context,…

Desktop app
G T A T C G C T A MeDUSA MeDUSA

MeDUSA

A computational pipeline bringing together numerous software packages to…

A computational pipeline bringing together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control (QC), and determination and…

Desktop app
G T A T C G C T A Methyl-Analyzer Methyl-Analyzer

Methyl-Analyzer

A python package that analyzes genome-wide DNA methylation data produced by the…

A python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-Analyzer processes and integrates…

Desktop app
G T A T C G C T A MetMap MetMap

MetMap

A computational pipeline for the analysis of MethylSeq experiments.

A computational pipeline for the analysis of MethylSeq experiments.

Desktop app
G T A T C G C T A MeQA MeQA

MeQA

We present a pipeline for the pre-processing, quality assessment, read…

We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets.

Desktop app
G T A T C G C T A DISMISS DISMISS

DISMISS

An R script, which as an additional step in MeDIP-Seq data analysis workflow,…

An R script, which as an additional step in MeDIP-Seq data analysis workflow, enables the allocation of strands to methylated DNA regions. DISMISS does this by analyzing the proportions of first mate…

Desktop app
G T A T C G C T A MethylAction MethylAction

MethylAction

An R package for detecting differentially methylated regions (DMRs) from…

An R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methylation genome-wide. These techniques include MBD-isolated Genome…

Desktop app
G T A T C G C T A BayMeth BayMeth

BayMeth

An empirical Bayes approach that uses a fully methylated control sample to…

An empirical Bayes approach that uses a fully methylated control sample to transform observed read counts into regional methylation levels. In our model, inefficient capture can readily be…

Desktop app
G T A T C G C T A Quantitative… Quantitative Sequencing Enrichment Analysis

QSEA Quantitative Sequencing Enrichment Analysis

Implements a statistical framework for modelling and transformation of…

Implements a statistical framework for modelling and transformation of MeDIP-seq enrichment data to absolute methylation levels similar to Bisulfite Sequencing (BS) read-outs. QSEA comprises…

Desktop app
G T A T C G C T A Strand NGS Strand NGS

Strand NGS

An integrated platform that provides analysis, management and visualization…

An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq,…

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