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
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 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
Analysing Illumina HumanMethylation BeadChip 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 Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze, manage and store bisulfite sequencing data
Analyze, manage and store whole-genome methylation 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
Assess epigenetic heterogeneity with proportion of intermediate methylation
Associates DNA Methylation with Matched gene Expression
Associates DNA Methylation with Matched gene Expression
Associates DNA Methylation with Matched gene Expression
A time series clustering package combining slope and Frechet distances
A time series clustering package combining slope and Frechet distances
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)
Automated functions for comparing various omic data from cbioportal.org
Automated functions for comparing various omic data from cbioportal.org
Automated functions for comparing various omic data from cbioportal.org
Base resolution DNA methylation data analysis
Base resolution DNA methylation data analysis
Bayesian clustering and imputationa of single cell methylomes
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
Bioconductor components for general cancer genomics
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
Bump Hunter
Bump Hunter
Bump Hunter
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Convenience Functions for Biscuit
Convenience Functions for Biscuit
Convenience Functions for Biscuit
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Correction of batch effects in DNA methylation data
Correction of batch effects in DNA methylation data
Correction of batch effects in DNA methylation data
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
Cross omic genetic fingerprinting
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
DeepBlueR
DeepBlueR
detect different methylation level (DMR)
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
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing 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
Differentially Methylated Regions caller
Discriminant Analysis for Evolutionary Inference
Discriminant Analysis for Evolutionary Inference
Dispersion shrinkage for sequencing data
Dispersion shrinkage for sequencing data
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA methylation analysis from high-throughput bisulfite sequencing results
DNA methylation analysis from high-throughput bisulfite sequencing results
DNA methylation analysis from high-throughput bisulfite sequencing results
DNA methylation analysis from high-throughput bisulfite sequencing results
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
Empirical Analysis of Digital Gene Expression Data in R
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
Epigenetic Dissection of Intra-Sample-Heterogeneity
Epigenomic tools
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
Estimate the cell composition of whole blood in DNA methylation samples
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
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 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
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Finds DAMEs - Differential Allelicly MEthylated regions
Finds DAMEs - Differential Allelicly MEthylated regions
Functions to conduct quality control analysis in methylation data
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
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEM: fast association study for the interplay of Gene, Environment and Methylation
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
Get CNV information from 450K array
Handle Illumina methylation data
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
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Illumina 450 and EPIC methylation array normalization and metrics
Illumina 450K methylation array spatial analysis methods
Illumina 450 methylation array normalization and metrics
Illumina HumanMethylation Manifest with shiny UI
Illumina HumanMethylation Manifest with shiny UI
Illumina methylation array analysis for large experiments
Illumina methylation array analysis for large experiments
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
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
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
Interface in R for the TCGA Portal
IP-seq data analysis and vizualization
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
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
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
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
MethylIT utility
MethyLiution: A QC Pipeline For Methylation Data
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
Missing Value Estimation of DNA Methylation Data
Model-based analysis of DNA methylation data
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Modelling Experimental Data from MeDIP Enrichment
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Muscle Epigenetic Age Test
Muscle Epigenetic Age Test
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
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
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Placental DNA methylation analysis tools
Placental DNA methylation analysis tools
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
Prediction of gestational age with Illumina HumanMethylation450 data
Prediction of gestational age with Illumina HumanMethylation450 data
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
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
Repetitive Element Methylation Prediction
RnBeads
Robust outlier identification for DNA methylation data
Robust outlier identification for DNA methylation data
R package for calling CNV from Illumina 450k methylation microarrays
Segmentation of Bis-seq data
Segmentation of Bis-seq data
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
ShinyÉPICo
Simplify production of computable OSCA texts and artifacts for AnVIL
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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
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
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
TFregulomeR reveals transcription factors’ context-specific features and functions
TFregulomeR reveals transcription factors’ context-specific features and functions
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
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
Tools for the analysis of heterogeneous tissues
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visualise methlation data from Oxford Nanopore sequencing
Visualization of Methylation Data
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip