Bioconductor Topics

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

BEAT - BS-Seq Epimutation Analysis Toolkit

Model higher-order methylation profiles

Bias-free Footprint Enrichment Test

Coordinate Covariation Analysis

Data companion to CTexploreR

Explores Cancer Testis Genes

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Analysis of single-cell epigenomics datasets with a Shiny App

Differential Enrichment Scan 2

Methylation array and sequencing spatial analysis methods

Differential Binding Analysis of ChIP-Seq Peak Data

Comparison, Benchmarking & QC of Epigenomic Datasets

Epigenetic Dissection of Intra-Sample-Heterogeneity

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

Efficient Power Analysis for EWAS with Continuous or Binary Outcomes

Evaluating SNV-Induced Disruption of G-Quadruplex Structures

Prediction of gestational age with Illumina HumanMethylation450 data

Binomial test for Hi-C data analysis

HiCaptuRe: Manipulating and integrating Capture Hi-C data

Hierarchical Inference of Spatial Positions from Hi-C Data

Integrative Statistics of alleLe Dependent Expression

Search for correlation between epigenetic signals and gene expression in TADs

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Muscle Epigenetic Age Test

Methylation-Based Inference of Regulatory Activity

Integrate microRNA and gene expression to decipher pathway complexity

Bayesian clustering and imputationa of single cell methylomes

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

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

Visualise methylation data from Oxford Nanopore sequencing

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Disk-backed Representation of ONT bedMethyl Files

Repetitive Element Methylation Prediction

RnBeads

Smooth modeling of bisulfite sequencing

Calculates cell type specificity from single cell data

Analysis tools for Single Molecule Footprinting (SMF) data

An R package to associate peaks and target genes

Time course sequencing data analysis

R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors

Tools for the analysis of heterogeneous tissues

Toolbox for mRNA epigenetics sequencing analysis

Call CNV from single cell ATAC-seq data based on InferCNV adaptation

Improved ChromVAR (Chromatin Variation Across Regions)

Bump Hunter

Automated functions for comparing various omic data from cbioportal.org