Biocview "DNAMethylation"

Adaptive Robust Regression normalization for Illumina methylation data
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 fast scatterplot smoother suitable for microarray normalization
All sample mean normalization.
Analyse, manage and visualise co-methylation data.
Analysing Illumina HumanMethylation BeadChip Data
Analysing Illumina HumanMethylation BeadChip Data
Analysis of DNA methylation data from CHARM microarrays
Analysis of DNA methylation data from CHARM microarrays
Analytical Tools for MassArray 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 bisulfite sequencing data
Analyze, manage and store bisulfite sequencing data
An R package to simulate DNA methylation data
Assess epigenetic heterogeneity with proportion of intermediate methylation
Assess epigenetic heterogeneity with proportion of intermediate methylation
Base resolution DNA methylation data analysis
Base resolution DNA methylation data analysis
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
BEAT - BS-Seq Epimutation Analysis Toolkit
BEAT - BS-Seq Epimutation Analysis Toolkit
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bump Hunter
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
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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Correct for batch effects in DNA methylation data
Correct for 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
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
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
DeepBlueR
DeepBlueR
DeepBlueR
DeepBlueR
detect different methylation level (DMR)
detect different methylation level (DMR)
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
(development for M3D) Identifies differentially methylated regions across testing groups
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Differential Methylation Analysis with Targeted Minimum Loss-Based Estimates of Variable Importance Measures
Dispersion shrinakge for sequencing data.
Dispersion shrinkage for sequencing data.
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
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 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 analysis from high-throughput bisulfite sequencing results
DNA methylation data analysis and visualization
DNA methylation data analysis and visualization
Efficient algorithms for DNA methylation
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Epigenetic Dissection of Intra-Sample-Heterogeneity
Epigenomic tools
Epigenomic tools
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
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 Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Functions to conduct quality control analysis in methylation data
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
GEM: fast association study for the interplay of Gene, Environment and Methylation
Get CNV information from 450K array
Handle Illumina methylation data
Handle Illumina methylation data
Handle Illumina methylation data
Identifies differentially methylated regions across testing groups
Identifies differentially methylated regions across testing groups
Identifying Differential Effects in Tiling Microarray Data
Identifying Differential Effects in Tiling Microarray Data
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 450K methylation array spatial analysis methods
Illumina 450 methylation array normalization and metrics
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
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
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Interactive visualization for Illumina methylation arrays
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
IP-seq data analysis and vizualization
MBDDiff for processing MBDcap-seq datasets
Methods for visualization and statistics on DNA methylation data
Methods for visualization and statistics on DNA methylation data
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 regulation network inference with Conditional Mutual information based PC-algorithem
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
Model-based analysis 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
Model higher-order methylation profiles
Modelling Experimental Data from MeDIP Enrichment
Modelling Experimental Data from MeDIP Enrichment
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Perform methylation analysis
Perform methylation analysis
Perform methylation analysis
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Prediction of gestational age with Illumina HumanMethylation450 data
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
Preprocessing of Illumina Infinium 450K data
Processing and analyzing bisulfite sequencing data
Processing and analyzing bisulfite sequencing data
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
RnBeads
RnBeads
R package for calling CNV from Illumina 450k methylation microarrays
R package for calling CNV from Illumina 450k methylation microarrays
Segmentation of Bis-seq data
Segmentation of Bis-seq data
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
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
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 HELP data analysis
Tools for HELP data analysis
Tools for region- and process-centric analyses of multiple assay types
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
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip