Biocview "Epigenetics"

A/B compartment inference from ATAC-seq and methylation array data

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

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

A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

A GAM based framework for analysis of ChIP-Seq data

Analysis of single-cell epigenomics datasets with a Shiny App

AnaLysis routines for ePigenomicS data

Analysis Tools for scATACseq Data with CoGAPS

Analysis tools for Single Molecule Footprinting (SMF) data

Analyze Illumina Infinium DNA methylation arrays

An R package for prediction of nucleosome positions

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

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package to detect chromatin state switches from epigenomic data

A package for the CLIP data visualization

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

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

Associates DNA Methylation with Matched gene Expression

Automated functions for comparing various omic data from cbioportal.org

Automatic calculation of literature relevance of genes

Bayesian clustering and imputationa of single cell methylomes

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BEAT - BS-Seq Epimutation Analysis Toolkit

Bias-free Footprint Enrichment Test

Binned Motif Enrichment Analysis and Visualization

Binomial test for Hi-C data analysis

Bump Hunter

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

ChIP-Seq data scaling according to spike-in control

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Companion package to chipenrich

Comparison, Benchmarking & QC of Epigenomic Datasets

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

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

Coordinate Covariation Analysis

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 (USC version)

DeepBlueR

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

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Differential Binding Analysis of ChIP-Seq Peak Data

Differential Enrichment Scan

Differential Enrichment Scan 2

Discriminant Analysis for Evolutionary Inference

Dunedin Pace of Aging Methylation Score Calculator based on Dunedin Age 45 data (DunedinPACE)

DynaMO predicts spatiotemporal binding of transcription factors

Empirical Analysis of Digital Gene Expression Data in R

Epigenetic Dissection of Intra-Sample-Heterogeneity

Epigenomic R-based analysis with hidden Markov models

epigenomic road map adventures

EpiMethEx Package

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

epiwraps: Wrappers for plotting and dealing with epigenomics data

Estimate Promoter Activity from RNA-Seq data

Estimate Systems Immune Response from RNA-seq data

Exploratory Analysis of ATAC-seq data

Exposome and omic data associatin and integration analysis

Fast, Epiallele-Aware Methylation Caller and Reporter

Finding differentially expressed unannotated genomic regions from RNA-seq data

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Generation of null ranges via bootstrapping or covariate matching

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Enrichment For ChIP-seq Peak Data

Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Identification of enriched motif pairs from chromatin interaction data

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

Imputation-guided re-construction of complete methylomes from WGBS data

Integrative Analysis and Visualization of Epigenomic Sequencing Data

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Irreproducible Discovery Rate for Genomic Interactions Data

Iterative Differential Clustering for single-cell

Linear Models for Microarray Data

m6Aboost

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

Methylated CpGs Set Enrichment Analysis

Methylation Analysis Based on Signal Detection

Methylation array and sequencing spatial analysis methods

Methylation-Based Inference of Regulatory Activity

MethylIT utility

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Model higher-order methylation profiles

msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Multi-Contrast Gene Set Enrichment Analysis

Muscle Epigenetic Age Test

Network Analysis Supported by Boosting

Perform co-DE gene analysis

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Placental DNA methylation analysis tools

Precict cis-co-accessibility from single-cell chromatin accessibility data

Predict cis-co-accessibility from single-cell chromatin accessibility data

Prediction of gestational age with Illumina HumanMethylation450 data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Quantifying the accuracy of cellular deconvolution

Repetitive Element Methylation Prediction

RLSeq: An analysis package for R-loop mapping data

RnBeads

R package for CRAG

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Search for correlation between epigenetic signals and gene expression in TADs

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Smooth modeling of bisulfite sequencing

StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub

Statistical analysis of RNA editing sites and hyper-editing regions

tensorICA

TFregulomeR reveals transcription factors’ context-specific features and functions

The data package associated with the MAGAR R-package

Tidy Meta Profiles using Bioconductor and the Tidyverse

Time course sequencing data analysis

Toolbox for mRNA epigenetics sequencing analysis

Tools for the analysis of heterogeneous tissues

Tornado Plot

Utilities for ATACseq QC, differential accessibility, and integration

Visualise methylation data from Oxford Nanopore sequencing

Visualization of Methylation Data

xcore expression regulators inference

Biocview "Epigenetics"

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