Biocview "MethylSeq"

A/B compartment inference from ATAC-seq and methylation array data
A/B compartment inference from ATAC-seq and methylation array data
A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis tools for Single Molecule Footprinting (SMF) 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
Association analysis of genomic regions based on permutation tests
Association analysis of genomic regions based on permutation tests
Base resolution DNA methylation data analysis
Base resolution DNA methylation data analysis
BEAT - BS-Seq Epimutation Analysis Toolkit
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
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
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 resource for package "TRESS"
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
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
Epigenomic tools
Epigenomic tools
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
Examine the Quality of Methylome Data
Example experimental data for use with the methyvim package
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
Fast, Epiallele-Aware Methylation Caller and Reporter
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
Guitar
Guitar
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
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
Peak Calling and differential analysis for MeRIP-Seq
Peak Calling and differential analysis for MeRIP-Seq
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
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information
Processing and analyzing bisulfite sequencing data
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
RnBeads
Segmentation of Bis-seq data
Segmentation of Bis-seq data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
systemPipeRdata: Workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: Workflow Environment for Data Analysis and Report Generation
Targeted, Robust, and Model-free Differential Methylation Analysis
Targeted, Robust, and Model-free Differential Methylation Analysis
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
Tools for analysing methylation patterns at genomic tuples
Transcriptome-guided quality assessment of m6A-seq data