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.
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…
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…
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…
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…
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…
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,…
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…
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…
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…
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…
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…
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.
A computational pipeline for the analysis of MethylSeq experiments.
A computational pipeline for the analysis of MethylSeq experiments.
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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