Biocview "DifferentialMethylation"

Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

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

Analysing Illumina HumanMethylation BeadChip Data

Analyze Illumina Infinium DNA methylation arrays

a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Bioc2019PanCancerStudy

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

ChIP-Seq data scaling according to spike-in control

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.

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

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

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Delineate outstanding genomic zones of differential gene activity

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

(development for M3D) Identifies differentially methylated regions across testing groups

Differential Epigenetic Coregulation Test

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated Regions caller

Differential methylation anlsysis for bisulfite sequencing data

Discriminant Analysis for Evolutionary Inference

Dispersion shrinkage for sequencing data

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

Empirical Analysis of Digital Gene Expression Data in R

Epigenetic Dissection of Intra-Sample-Heterogeneity

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Example experimental data for use with the methyvim package

Exposome and omic data associatin and integration analysis

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Finds DAMEs - Differential Allelicly MEthylated regions

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Gene Set Analysis Using the Outcome of Differential Methylation

Identification of Functional Epigenetic Modules

Identifies differentially methylated regions across testing groups

Identify oncogenes and tumor suppressor genes from omics data

Illumina 450K methylation array spatial analysis methods

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Inferring unobserved perturbations from gene expression data

Interval-Wise Testing for Omics Data

IP-seq data analysis and vizualization

Lite version of EpigenCentral

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

Methylated CpGs Set Enrichment Analysis

Methylation Analysis Based on Signal Detection

Methylation array and sequencing spatial analysis methods

MethylIT utility

MethylMix: Identifying methylation driven cancer genes

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

Placental DNA methylation analysis tools

Processing Various Types of Data on GEO and TCGA

Quality control and analysis tools for Illumina DNA methylation BeadChip

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Repetitive Element Methylation Prediction

RnBeads

ShinyÉPICo

Significance-based Modules Integrating the Transcriptome and Epigenome

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Smooth modeling of bisulfite sequencing

Spike-in calibration for cell-free MeDIP

Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

Targeted, Robust, and Model-free Differential Methylation Analysis

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

tensorICA

Toolbox for mRNA epigenetics sequencing analysis

Tools for the analysis of heterogeneous tissues

Visualise methlation data from Oxford Nanopore sequencing

Visualise methylation data from Oxford Nanopore sequencing

Biocview "DifferentialMethylation"

R Package Documentation

Browse R Packages

We want your feedback!