Biocview "DNAMethylation"

Access and Analyze DNA Methylation Array Databases

Access and analyze public DNA methylation array data compilations

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

Adaptive Robust Regression normalization for Illumina methylation data

A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

A fast scatterplot smoother suitable for microarray normalization

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

Analyse, manage and visualise co-methylation data.

Analysing Illumina HumanMethylation BeadChip Data

Analysis of DNA methylation data from CHARM microarrays

Analysis tools for Single Molecule Footprinting (SMF) data

Analytical Tools for MassArray Data

Analyze Illumina Infinium DNA methylation arrays

Analyze, manage and store bisulfite sequencing data

Analyze, manage and store whole-genome methylation data

An R package to simulate DNA methylation data

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

Assess epigenetic heterogeneity with proportion of intermediate methylation

Associates DNA Methylation with Matched gene Expression

A time series clustering package combining slope and Frechet distances

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

Automated functions for comparing various omic data from cbioportal.org

Base resolution DNA methylation data analysis

Bayesian clustering and imputationa of single cell methylomes

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

BEAT - BS-Seq Epimutation Analysis Toolkit

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Bioc2019PanCancerStudy

Bioconductor components for general cancer genomics

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Bump Hunter

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

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

Correction of batch effects in DNA methylation data

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

Cross omic genetic fingerprinting

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

DataSHIELD client site Omics association functions.

DataSHIELD server site Omic functions

DeepBlueR

detect different methylation level (DMR)

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

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

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

Differential Epigenetic Coregulation Test

Differentially Methylated Regions caller

Discriminant Analysis for Evolutionary Inference

Dispersion shrinkage for sequencing data

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

DNA IP-seq data analysis

DNA methylation analysis from high-throughput bisulfite sequencing results

DNA methylation data analysis and visualization

DNA methylation exposure and phenotypic archive

Efficient algorithms for DNA methylation

Efficient and Flexible EWAS

Empirical Analysis of Digital Gene Expression Data in R

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Epigenetic Dissection of Intra-Sample-Heterogeneity

Epigenomic tools

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

Estimate the cell composition of whole blood in DNA methylation samples

Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

Example datasets of input data for shinyMethyl

Example experimental data for use with the methyvim package

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Fast and efficient summarization of single cell whole genome bisulfate data

Fast, Epiallele-Aware Methylation Caller and Reporter

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Finds DAMEs - Differential Allelicly MEthylated regions

Functions to conduct quality control analysis in methylation data

Functions used to preprocess datasets stored in BioDataome

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

Gene Set Analysis Using the Outcome of Differential Methylation

Get CNV information from 450K array

Handle Illumina methylation data

Identifies differentially methylated regions across testing groups

Identifying Differential Effects in Tiling Microarray Data

Identifying differentially methylated regions efficiently with power and control

Identify oncogenes and tumor suppressor genes from omics data

Illumina 450K methylation array spatial analysis methods

Illumina 450 methylation array normalization and metrics

Illumina DNA methylation array normalization and metrics

Illumina HumanMethylation Manifest with shiny UI

Illumina methylation array analysis for large experiments

Imputation-guided re-construction of complete methylomes from WGBS data

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Integrative analysis of multi-omics data to infer regulatory networks

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Interactive visualization for Illumina methylation arrays

Interface in R for the TCGA Portal

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

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

MBDDiff for processing MBDcap-seq datasets

Methods for visualization and statistics on DNA methylation data

Methylated CpGs Set Enrichment Analysis

Methylation Analysis Based on Signal Detection

Methylation array and sequencing spatial analysis methods

Methylation-Based Inference of Regulatory Activity

MethylIT utility

MethyLiution: A QC Pipeline For Methylation Data

MethylMix: Identifying methylation driven cancer genes

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Missing Value Estimation of DNA Methylation Data

Model-based analysis of DNA methylation data

Model higher-order methylation profiles

Modelling Experimental Data from MeDIP Enrichment

Multi-Contrast Gene Set Enrichment Analysis

Muscle Epigenetic Age Test

Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Perform methylation analysis

Perform methylation analysis and facilitates differential expression analyses

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

Placental DNA methylation analysis tools

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Prediction of gestational age with Illumina HumanMethylation450 data

Preprocessing of Illumina Infinium 450K data

probability illustrations with playing cards

Processing and analyzing bisulfite sequencing data

Processing Various Types of Data on GEO and TCGA

QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quantifying the accuracy of cellular deconvolution

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

Repetitive Element Methylation Prediction

RnBeads

Robust outlier identification for DNA methylation data

R package for calling CNV from Illumina 450k methylation microarrays

Segmentation of Bis-seq data

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

ShinyÉPICo

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulation and Deconvolution of Omic Profiles

Smooth modeling of bisulfite sequencing

Spike-in calibration for cell-free MeDIP

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

TFregulomeR reveals transcription factors’ context-specific features and functions

The Cancer Genome Atlas Data Integration

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Tools for analysing methylation patterns at genomic tuples

Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Tools for HELP data analysis

Tools for region- and process-centric analyses of multiple assay types

Tools for the analysis of heterogeneous tissues

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Visualise methylation data from Oxford Nanopore sequencing

Visualization of Methylation Data

Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Biocview "DNAMethylation"

R Package Documentation

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