Bioconductor Packages

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Coordinate Covariation Analysis

Statistical tools for the analysis of ChIP-seq data

Chip-seq Signal Quantifier Pipeline

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Simulation of ChIP-seq experiments

Analysis of single-cell epigenomics datasets with a Shiny App

Differential gene expression analysis based on the negative binomial distribution

Probabilistic association of DEGs to CREs from differential data

Comparison, Benchmarking & QC of Epigenomic Datasets

find influential TF and Target based on multi-omics data

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Plot profiles of next generation sequencing data in genomic features

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Set of 3D genomic interaction analysis tools

Search for correlation between epigenetic signals and gene expression in TADs

Locus overlap analysis for enrichment of genomic ranges

Learning from DNA to Predict Enhancers

Linear model and normality based normalization and transformation method (Linnorm)

MACS: Model-based Analysis for ChIP-Seq

DNA IP-seq data analysis

Methylation-Based Inference of Regulatory Activity

Statistical Testing for ChIP-Seq data sets

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

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

Quantify and Annotate Short Reads in R

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Replicate oriented Visualization of a genomic region

Mapping, quantification and variant analysis of sequencing data

An example dataset for use with the SVM2CRM package

An R package to associate peaks and target genes

Time course sequencing data analysis

TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

Transcription Factor High Accumulation Zones

Differential cell-type-specific allelic imbalance

Affinity test for identifying regulatory SNPs

Gene Set Enrichment For ChIP-seq Peak Data

Companion package to chipenrich

chipseq: A package for analyzing chipseq data

A package for the CLIP data visualization