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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.

RnBeads
Desktop

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…

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MEDME
Desktop

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…

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Repitools
Desktop

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,…

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MEDIPS
Desktop

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…

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QSEA
Desktop

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…

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MethylAction
Desktop

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…

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BioVLAB-mCpG-SN…
Web

BioVLAB-mCpG-SNP-EXPRESS

Enables to examine the multi-omics integrated analysis and supplies users a way…

Enables to examine the multi-omics integrated analysis and supplies users a way to study their own multi-omics data. It works on the integrated analysis of gene expression, DNA methylation, and…

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DISMISS
Desktop

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…

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MeDUSA
Desktop

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…

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Methyl-Analyzer
Desktop

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…

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MeQA
Desktop

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.

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Strand NGS
Desktop

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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MetMap
Desktop

MetMap

Infers methylation at individual CGs by modelling biases inherent in MethylSeq…

Infers methylation at individual CGs by modelling biases inherent in MethylSeq experiments. MetaMap is a statistical method that first accounts for the biases in MethylSeq data and then generates an…

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