Biocview "Epigenetics"

A/B compartment inference from ATAC-seq and methylation array data
A/B compartment inference from ATAC-seq and methylation array data
A/B compartment inference from ATAC-seq and methylation array data
Access and analyze the Recount Methylation database
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 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
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
AnaLysis routines for ePigenomicS data
AnaLysis routines for ePigenomicS data
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
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 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 for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
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
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
Assess epigenetic heterogeneity with proportion of intermediate methylation
Assess epigenetic heterogeneity with proportion of intermediate methylation
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
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
BEAT - BS-Seq Epimutation Analysis Toolkit
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
Binomial test for Hi-C data analysis
Binomial test for Hi-C data analysis
Bump Hunter
Bump Hunter
Bump Hunter
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
ChIP-Seq data scaling according to spike-in control
ChIP-Seq data scaling according to spike-in control
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Companion package to chipenrich
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
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
Cross omic genetic fingerprinting
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 (USC version)
DeepBlueR
DeepBlueR
DeepBlueR
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Differential Enrichment Scan
Differential Enrichment Scan 2
Differential Enrichment Scan 2
DMR calculation
DynaMO predicts spatiotemporal binding of transcription factors
Empirical Analysis of Digital Gene Expression Data in R
Epigenetic Dissection of Intra-Sample-Heterogeneity
Epigenetic Dissection of Intra-Sample-Heterogeneity
epigenomic road map adventures
EpiMethEx Package
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
Finding differentially expressed unannotated genomic regions from RNA-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Gene Set Enrichment For ChIP-seq Peak Data
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
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Statistics of alleLe Dependent Expression
Irreproducible Discovery Rate for Genomic Interactions Data
Irreproducible Discovery Rate for Genomic Interactions Data
Linear Models for Microarray Data
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
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-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
MethylIT utility
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Muscle Epigenetic Age Test
Network Analysis Supported by Boosting
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
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility 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
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
RnBeads
Search for correlation between epigenetic signals and gene expression in TADs
Search for correlation between epigenetic signals and gene expression in TADs
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
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
Tidy Meta Profiles using Bioconductor and the Tidyverse
Time course sequencing data analysis
Time course sequencing data analysis
Tools for the analysis of heterogeneous tissues
Tools for the analysis of heterogeneous tissues
Utilities for ATACseq QC, differential accessibility, and integration