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
Analysing Illumina HumanMethylation BeadChip Data
Analysing Illumina HumanMethylation BeadChip Data
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bioc2019PanCancerStudy
ChIP-Seq data scaling according to spike-in control
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
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
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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
(development for M3D) Identifies differentially methylated regions across testing groups
Differential Epigenetic Coregulation Test
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Differential methylation anlsysis for bisulfite sequencing data
Differential methylation anlsysis for bisulfite sequencing data
Differential methylation anlsysis for bisulfite sequencing data
Dispersion shrinkage for sequencing data
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
Epigenetic Dissection of Intra-Sample-Heterogeneity
Example experimental data for use with the methyvim package
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Finds DAMEs - Differential Allelicly MEthylated regions
Finds DAMEs - Differential Allelicly MEthylated regions
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
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
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
Interval-Wise Testing for Omics Data
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Methylated CpGs Set Enrichment Analysis
Methylated CpGs Set Enrichment Analysis
Methylation Analysis Based on Signal Detection
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
MethylIT utility
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
pinnacle: Gene set enrichment analysis based on genomic intervals
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
RnBeads
ShinyEPICO!
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Targeted, Robust, and Model-free Differential Methylation Analysis
Targeted, Robust, and Model-free Differential Methylation Analysis
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
tensorICA
Tools for the analysis of heterogeneous tissues
Tools for the analysis of heterogeneous tissues