Biocview "ChIPSeq"

Additional functions for working with ChIP-Seq data

Affinity test for identifying regularity Indels

Affinity test for identifying regulatory SNPs

A GAM based framework for analysis of ChIP-Seq data

A graphical interface for the metagene package

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis of single-cell epigenomics datasets with a Shiny App

AnaLysis routines for ePigenomicS data

Analyze Transcription Factor Enrichment

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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

An R package for the creation of complex genomic profile plots

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

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

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

A package for the CLIP data visualization

A package to produce metagene plots

Application of t-sne to NGS Genomic Signal Profiles

Association analysis of genomic regions based on permutation tests

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

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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

Bayesian Analysis of ChIP-seq Data

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

Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

ChIP-Seq Analysis with Windows

chipseq: A package for analyzing chipseq data

ChIP-Seq data scaling according to spike-in control

Chip-seq Signal Quantifier Pipeline

ChIP-Seq Statistical Power

ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures

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

chroGPS2: Generation, visualization and differential analysis of epigenome maps

Clustering and Alignment of ChIP-Seq peaks based on their shapes

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

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

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.

Companion package to chipenrich

Comparison, Benchmarking & QC of Epigenomic Datasets

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

ComSeq: An ensemble method for RNA-Seq differential analysis

Coordinate Covariation Analysis

Coverage visualization package for R

DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

de novo motif discovery

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

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Differential Binding Analysis of ChIP-Seq Peak Data

Differential Binding Estimation for Protein Complexes

Differential Binding of Transcription Factor with ChIP-seq

Differential cell-type-specific allelic imbalance

Differential Epigenetic Coregulation Test

Differential gene expression analysis based on the negative binomial distribution

Discriminant Analysis for Evolutionary Inference

DNA IP-seq data analysis

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

DynaMO predicts spatiotemporal binding of transcription factors

Empirical Analysis of Digital Gene Expression Data in R

Epigenetic and gene transcription data normalization and integration with mixture models

Epigenomic R-based analysis with hidden Markov models

epigenomic road map adventures

Experimental Design in Differential Abundance analysis

find influential TF and Target based on multi-omics data

Finding Co-occuring motifs of transcription factor binding sites

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

Functionality Visualization for Motifs

GC Aware Peak Caller

Generation of null ranges via bootstrapping or covariate matching

Gene Set Enrichment For ChIP-seq Peak Data

GeneSet objects from ChIP-Seq experiments

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

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Heatmaps of Stack Profiles from Epigenetic Signals

Hi-C Annotation and Graphics Ensemble

iASeq: integrating multiple sequencing datasets for detecting allele-specific events

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Infrastructure for microfluidic oscillatory washing-based ChIP

Interactive Differential Expresion Analysis Browser

IP-seq data analysis and vizualization

Iterative Differential Clustering for single-cell

Learning from DNA to Predict Enhancers

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

Locus overlap analysis for enrichment of genomic ranges

MACS: Model-based Analysis for ChIP-Seq

Make read coverage plots from BigWig files

Mapping, quantification and variant analysis of sequencing data

Maximum rank reproducibility

Methylation-Based Inference of Regulatory Activity

Metrics to estimate a level of similarity between two ChIP-Seq profiles

Motif Identification and Validation

Motifs in Tandem with One Another

Multiple Sample Peak Calling

Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data

Normalization and difference calling in ChIP-seq data

Nucleosome positioning package for R

Optimized Functional Annotation Of ChIP-seq Data

Peak Refinement Metric Gathering and Evalutation by Motif Enrichment

Peak saturation processing and analysis

Plot customizable linear genomes displaying arbitrary data

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Power Estimation Tool for RNA-Seq and proteomics data

QC for enrichment based NGS

Quality Control Pipeline for ChIP-Seq Data

Quality metrics for ChIPseq data

Quantify and Annotate Short Reads in R

Quantifying Differential Features

Quantitative comparison of multiple ChIP-seq datasets

R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Recipes using seqsetvis

Replicate oriented Visualization of a genomic region

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Search for correlation between epigenetic signals and gene expression in TADs

Segvis: A package for visualization of high throughput sequencing data along genomic segments

Set Based Visualizations for Next-Gen Sequencing Data

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

Simulation of ChIP-seq experiments

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

Statistical Testing for ChIP-Seq data sets

Statistical tools for the analysis of ChIP-seq data

SVM2CRM: support vector machine for cis-regulatory elements detections

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

TFregulomeR reveals transcription factors’ context-specific features and functions

The Genomic STate ANnotation Package

Time course sequencing data analysis

Tools for the Efficient Analysis of High-Resolution Genomics Data

Transcription Factor High Accumulation Zones

Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data

VirtUaL ChIP-Seq data Analysis using Networks

Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Visualization and annotation of read signal over genomic ranges with profileplyr

Biocview "ChIPSeq"

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