Biocview "MethylSeq"

A/B compartment inference from ATAC-seq and methylation array data

A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Analysis of single-cell epigenomics datasets with a Shiny App

Analysis tools for Single Molecule Footprinting (SMF) data

An R package to simulate DNA methylation data

Assess epigenetic heterogeneity with proportion of intermediate methylation

Association analysis of genomic regions based on permutation tests

Base resolution DNA methylation data analysis

BEAT - BS-Seq Epimutation Analysis Toolkit

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

Convenience Functions for Biscuit

Coordinate Covariation Analysis

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Data resource for package "TRESS"

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

DNA methylation analysis from high-throughput bisulfite sequencing results

Epigenomic tools

Estimate the cell composition of whole blood in DNA methylation samples

Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

Examine the Quality of Methylome Data

Example experimental data for use with the methyvim package

exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

Fast, Epiallele-Aware Methylation Caller and Reporter

GEM: fast association study for the interplay of Gene, Environment and Methylation

Guitar

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Locus overlap analysis for enrichment of genomic ranges

m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Methylation-Based Inference of Regulatory Activity

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Peak Calling and differential analysis for MeRIP-Seq

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Plot customizable linear genomes displaying arbitrary data

Predicting context-specific m6A regulation of gene expression

Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information

Processing and analyzing bisulfite sequencing data

Quantify and Annotate Short Reads in R

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

RnBeads

Segmentation of Bis-seq data

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Targeted, Robust, and Model-free Differential Methylation Analysis

TFregulomeR reveals transcription factors’ context-specific features and functions

Tools for analysing methylation patterns at genomic tuples

Transcriptome-guided quality assessment of m6A-seq data

Biocview "MethylSeq"

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