Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Peak calling software tools | ChIP sequencing data analysis

Identification of genomic regions of interest in ChIP-seq data, commonly referred to as peak-calling, aims to find the locations of transcription factor binding sites, modified histones or nucleosomes.Source text:(Cairns et al., 2011) BayesPeak--an…
G T A T C G C T A
MACS
Desktop

MACS Model-based Analysis for ChIP-Seq

A software to analyze data generated by short read sequencers. MACS empirically…

A software to analyze data generated by short read sequencers. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. It…

G T A T C G C T A
HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

G T A T C G C T A
SICER
Desktop

SICER

A clustering approach for identification of enriched domains from histone…

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

G T A T C G C T A
SPP
Desktop

SPP

An R package for analysis of ChIP-seq and other functional sequencing data. SPP…

An R package for analysis of ChIP-seq and other functional sequencing data. SPP has been designed to detect protein binding positions with high accuracy. SPP can also examine the saturation level of…

G T A T C G C T A
Scripture
Desktop

Scripture

A method for transcriptome reconstruction that relies solely on RNA-Seq reads…

A method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage…

G T A T C G C T A
PeakSeq
Desktop

PeakSeq

A program for identifying and ranking peak regions in ChIP-Seq experiments.

A program for identifying and ranking peak regions in ChIP-Seq experiments.

G T A T C G C T A
F-Seq
Desktop

F-Seq

A software package that generates a continuous tag sequence density estimation…

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome…

G T A T C G C T A
QuEST
Desktop

QuEST

A Kernel Density Estimator-based package for analysis of massively parallel…

A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations.

G T A T C G C T A
DFilter
Desktop

DFilter

A detection algorithm that identifies regulatory features in ChIP-seq,…

A detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. The mathematical formalism underlying DFilter…

G T A T C G C T A
PFMS
Desktop

PFMS Peak-Finder MetaServer

A metaServer application designed for analyzing ChIP-seq data. It integrates…

A metaServer application designed for analyzing ChIP-seq data. It integrates several peak-finders within a single interface. A ChIP-seq data file can be analyzed using one or more of the peak-finders…

G T A T C G C T A
GeneProf
Web

GeneProf

A web-based, graphical software suite that allows users to analyse data…

A web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq).

G T A T C G C T A
FindPeaks
Desktop

FindPeaks

It can be used for converting Eland, Maq (.map), BED or other files into WIG…

It can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis). It is now being maintained as part of the open source…

G T A T C G C T A
Jmosaics
Desktop

Jmosaics

A probabilistic method for jointly analyzing multiple ChIP-seq datasets.…

A probabilistic method for jointly analyzing multiple ChIP-seq datasets. jMOSAiCS (joint model-based one- and two-sample analysis and inference for ChIP-seq) is a probabilistic model for integrating…

G T A T C G C T A
DANPOS
Desktop

DANPOS Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing

A comprehensive bioinformatics pipeline explicitly designed for dynamic…

A comprehensive bioinformatics pipeline explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. DANPOS is also robust in defining functional dynamic nucleosomes, not only…

G T A T C G C T A
CSDeconv
Desktop

CSDeconv

Maps transcription factor binding sites from ChIP-seq data to high resolution…

Maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.

G T A T C G C T A
BayesPeak
Desktop

BayesPeak

Provides a flexible implementation of the BayesPeak algorithm and is compatible…

Provides a flexible implementation of the BayesPeak algorithm and is compatible with downstream BioConductor packages. The BayesPeak package introduces a new method for summarizing posterior…

G T A T C G C T A
BroadPeak
Desktop

BroadPeak

Identifies broad peaks in diffuse ChIP-seq datasets. BroadPeak is a distinct…

Identifies broad peaks in diffuse ChIP-seq datasets. BroadPeak is a distinct approach for calling broad peaks in diffuse ChIP-seq datasets, and able to apply the algorithm to both real and simulated…

G T A T C G C T A
EDD
Desktop

EDD Enriched Domain Detector

Allows discovery of broad genomic enrichment areas from ChIP-seq data. EDD is a…

Allows discovery of broad genomic enrichment areas from ChIP-seq data. EDD is a genomic domain caller designed to detect megabase-size domains. The software enables quantitative analysis of ChIP-seq…

G T A T C G C T A
Peakzilla
Desktop

Peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq and…

An algorithm to identify transcription factor binding sites from ChIP-seq and ChIP-exo data.

G T A T C G C T A
CSAR
Desktop

CSAR ChIP-Seq Analysis in R

An R package for the statistical analysis of ChIP-seq experiments. CSAR…

An R package for the statistical analysis of ChIP-seq experiments. CSAR calculates single-nucleotide read-enrichment values, taking the average size of DNA fragments subjected to sequencing into…

G T A T C G C T A
COPAR
Desktop

COPAR ChIP-seq Optimal Peak AnalyzeR

Measures Next-generation sequencing (NGS)/ChIP-seq experiment quality through…

Measures Next-generation sequencing (NGS)/ChIP-seq experiment quality through global peak alignment comparison. COPAR can extract genomic features based on spectrum method for in-depth analysis of…

G T A T C G C T A
RSEG software
Desktop

RSEG software

The software package is aimed to analyze ChIP-Seq data, especially for…

The software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.

G T A T C G C T A
PICS
Desktop

PICS Probabilistic Inference for ChIP-Seq

A package for identifying regions bound by transcription factors from aligned…

A package for identifying regions bound by transcription factors from aligned reads. PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA…

G T A T C G C T A
DROMPA
Desktop

DROMPA DRaw and Observe Multiple enrichment Profiles and Annotation

Allows peak calling, visualization, quality check and Polymerase Chain Reaction…

Allows peak calling, visualization, quality check and Polymerase Chain Reaction (PCR) bias filtering of ChIP-seq data. DROMPA calls peaks by comparing the read distribution of the ChIP sample with…

G T A T C G C T A
PeakRanger
Desktop

PeakRanger

A peak-caller package that works equally well on punctate and broad sites.…

A peak-caller package that works equally well on punctate and broad sites. PeakRanger can resolve closely-spaced peaks, has excellent performance, and is easily customized. It can be run in a…

SigSeeker
Web

SigSeeker

Uses multiple tools to identify peaks. SigSeeker works about existing peak…

Uses multiple tools to identify peaks. SigSeeker works about existing peak comparisons by including peak overlaps of varying minimal width and peak-intensity correlation models. This is done to…

G T A T C G C T A
JAMM
Desktop

JAMM Joint Analysis of NGS replicates via Mixture Model clustering

A peak finder that can integrate information from biological replicates,…

A peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is…

G T A T C G C T A
GEM
Desktop

GEM Genome wide Event finding and Motif discovery

Allows investigation of protein-DNA interaction by ChIP-Seq/ChIP-exo data. GEM…

Allows investigation of protein-DNA interaction by ChIP-Seq/ChIP-exo data. GEM is based on an integrative computational method and intends to provide both improved spatial accuracy of binding event…

G T A T C G C T A
Q
Desktop

Q

A saturation-based ChIP-seq peak caller. Q uses an assessment of the quadratic…

A saturation-based ChIP-seq peak caller. Q uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by…

G T A T C G C T A
bPeaks
Desktop

bPeaks

Permits to detect transcription factor binding sites (TFBS) from ChIPseq data.…

Permits to detect transcription factor binding sites (TFBS) from ChIPseq data. bPeaks uses simple parameters to identify peaks, which actually correspond to the parameters that a user is considering…

G T A T C G C T A
HPeak
Desktop

HPeak

This program is for the purpose of defining genome-wide ChIP-enriched peaks in…

This program is for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads. The underlying algorithm is based on a two-state HMM.

G T A T C G C T A
Triform
Desktop

Triform

Automatics peak finding in ChIP-Seq enrichment profiles for transcription…

Automatics peak finding in ChIP-Seq enrichment profiles for transcription factors. Triform is a software which improves peak finding by identifying and using essential features of typical ChIP-Seq…

G T A T C G C T A
Pique
Desktop

Pique

Identifies protein–DNA binding events in small bacterial and archaeal…

Identifies protein–DNA binding events in small bacterial and archaeal genomes. Pique integrates with the Gaggle toolkit to facilitate downstream data visualization, curation and analysis. It also…

G T A T C G C T A
PeakError
Desktop

PeakError

Computes the annotation error of peak calls. PeakError allows, after…

Computes the annotation error of peak calls. PeakError allows, after constructing a database of annotated regions that represent your visual interpretation of the peak locations in a ChIP-seq…

G T A T C G C T A
Zerone
Desktop

Zerone

A ChIP-seq discretizer with built-in quality control. Zerone is powered by a…

A ChIP-seq discretizer with built-in quality control. Zerone is powered by a hidden Markov model with zero-inflated negative multinomial emissions, which allows it to merge several replicates into a…

G T A T C G C T A
Pasha
Desktop

Pasha Preprocessing of Aligned Sequences from HTS Analyses

An R package designed for processing aligned reads from chromatin-oriented…

An R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha allows easy manipulation of aligned reads from short-read sequencing…

G T A T C G C T A
BRACIL
Desktop

BRACIL Binding Resolution Amplifier and Cooperative Interaction Locator

Improves binding site resolution and predicts cooperative interactions. BRACIL…

Improves binding site resolution and predicts cooperative interactions. BRACIL can study physical properties of DNA shearing from the ChIP-seq coverage. It incorporates motif discovery and is able to…

G T A T C G C T A
OccuPeak
Desktop

OccuPeak

A peak-calling algorithm. OccuPeak uses the abundant low frequency tags present…

A peak-calling algorithm. OccuPeak uses the abundant low frequency tags present in each ChIP-seq dataset to model the background, thereby avoiding the need for additional datasets. Analysis of the…

G T A T C G C T A
BonnetEtAl2017
Nontypeable

BonnetEtAl2017

Quantifies spatial interactions between replication origins and chromatin…

Quantifies spatial interactions between replication origins and chromatin marks. This model provides a process used to explore the spatial interaction landscape of replication origins with their…

G T A T C G C T A
polyaPeak
Desktop

polyaPeak

An R package for ranking ChIP-seq peaks with shape information. polyaPeak uses…

An R package for ranking ChIP-seq peaks with shape information. polyaPeak uses a Bayesian hierarchical model to incorporate the peak shapes in the ranking. The shapes are described by a mixture of…

G T A T C G C T A
dPeak
Desktop

dPeak

A high resolution transcription factor binding site (TFBS) identification…

A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm.

G T A T C G C T A
MSPC
Desktop

MSPC

A general methodological framework to rigorously combine the evidence of…

A general methodological framework to rigorously combine the evidence of enriched regions in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a…

G T A T C G C T A
Sierra platinum
Desktop

Sierra platinum

Allows peak-calling of replicated ChIP-seq experiments. Sierra platinum…

Allows peak-calling of replicated ChIP-seq experiments. Sierra platinum provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and…

G T A T C G C T A
hiddenDomains
Desktop

hiddenDomains

Uses a hidden Markov model, to identify both enriched peaks and domains…

Uses a hidden Markov model, to identify both enriched peaks and domains simultaneously. It is unique in that it does not need to be tuned to one type of enrichment prior to analysis and does not make…

G T A T C G C T A
SIPeS
Desktop

SIPeS Site Identification from Paired-end Sequencing

Uses a dynamic baseline directly through the piling up of fragments to…

Uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end…

G T A T C G C T A
SISSRs
Desktop

SISSRs Site Identification from Short Sequence Reads

A novel algorithm for precise identification of binding sites from short reads…

A novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

G T A T C G C T A
PePr
Desktop

PePr Peak Prioritization pipeline

A ChIP-seq peak-calling and prioritization pipeline that uses a sliding window…

A ChIP-seq peak-calling and prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution. PePr…

G T A T C G C T A
MOSAiCS
Desktop

MOSAiCS MOdel-based one and two Sample Analysis and inference for ChIP-Seq Data

A statistical protocol for analyzing ChIP-seq data. Based on careful…

A statistical protocol for analyzing ChIP-seq data. Based on careful investigation of biases in ChIP-seq data such as mappability and GC content, MOSAiCS has been developed as a flexible mixture…

G T A T C G C T A
BiSA
Desktop

BiSA Binding Sites Analyser

Identifies genes located near binding regions of interest, genomic features…

Identifies genes located near binding regions of interest, genomic features near a gene or locus of interest and statistical significance of overlapping regions can also be reported. BiSA is a…

G T A T C G C T A
AREM
Desktop

AREM Aligning Reads by Expectation Maximization

An expectation-maximization (E-M) algorithm to update the alignment…

An expectation-maximization (E-M) algorithm to update the alignment probabilities of each read to different genomic locations. AREM takes the classic peak calling algorithm used in MACS 1.4 and adds…

G T A T C G C T A
T-KDE
Desktop

T-KDE

An efficient and effective method to predict constitutive protein binding sites…

An efficient and effective method to predict constitutive protein binding sites using ChIP-seq peaks from multiple cell lines. Besides constitutive binding sites for a given protein, T-KDE can…

G T A T C G C T A
NEXT-peak
Desktop

NEXT-peak

A program to call peaks from ChIP-seq data for transcription factor binding…

A program to call peaks from ChIP-seq data for transcription factor binding sites.

G T A T C G C T A
SWEMBL
Desktop

SWEMBL

Calls peaks from genomic data aligned to a reference genome. SWEMBL is based on…

Calls peaks from genomic data aligned to a reference genome. SWEMBL is based on a Markov chain in both strand directions. It identifies enriched intervals from data sets sorted by a numerical index.…

G T A T C G C T A
Ritornello
Desktop

Ritornello

Calls binding events without the need to do a pair total DNA input or IgG…

Calls binding events without the need to do a pair total DNA input or IgG control sample. Ritornello generally performs equally or better than the peak callers tested and recommended by the ENCODE…

G T A T C G C T A
peakrots
Desktop

peakrots

A tool for optimized ChIP-seq peak detection. Peakrots implements the ROTS…

A tool for optimized ChIP-seq peak detection. Peakrots implements the ROTS procedure for optimized ChIP-seq peak detection. It allows optimizing the binding site detections in a given ChIP-seq…

G T A T C G C T A
NarrowPeaks
Desktop

NarrowPeaks

Applies a functional version of principal component analysis (FPCA) to: (1)…

Applies a functional version of principal component analysis (FPCA) to: (1) Postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of…

G T A T C G C T A
DuffyTools
Desktop

DuffyTools

Uses as an R package for ChIP-seq peak filtering. DuffyTools provides useful…

Uses as an R package for ChIP-seq peak filtering. DuffyTools provides useful tools and genome annotations for processing Plasmodium and mammalian host genomic data sets.

G T A T C G C T A
DuffyNGS
Desktop

DuffyNGS

Uses for alignment and peak calling of ChIP-seq data. DuffyNGS is a package of…

Uses for alignment and peak calling of ChIP-seq data. DuffyNGS is a package of functions used to analyze mixed organism Next Generation Sequencing (NGS) data, typically RNA-seq.

G T A T C G C T A
epic
Desktop

epic

Finds medium to diffusely enriched domains in chip-seq data. epic is a fast,…

Finds medium to diffusely enriched domains in chip-seq data. epic is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm. It can use one core per…

G T A T C G C T A
HATSEQ
Desktop

HATSEQ Hypergeometric Analysis of Tiling-array and SEQuence data

A powerful tool that accurately identifies functional regions of interest…

A powerful tool that accurately identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. HATSEQ also…

G T A T C G C T A
Genomatix…
Desktop

Genomatix Software Suite

Allows analysis of genomic data. Genomatix Software Suite is a software that…

Allows analysis of genomic data. Genomatix Software Suite is a software that allows analysis of gene regulation and expression, generation and evaluation of network and pathways and visualization of…

G T A T C G C T A
qips
Desktop

qips

It finds enriched regions of arbitrary lengths and is therefore especially…

It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.

G T A T C G C T A
ERANGE
Desktop

ERANGE Enhanced Read Analysis of Gene Expression

A software tool for mapping and quantifying Mammalian transcriptomes by…

A software tool for mapping and quantifying Mammalian transcriptomes by RNA-Seq. The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads…

G T A T C G C T A
ZINBA
Desktop

ZINBA Zero-Inflated Negative Binomial Algorithm

A flexible statistical framework capable of identifying regions of enrichment…

A flexible statistical framework capable of identifying regions of enrichment across a wide variety of DNA-seq data types, enrichment patterns, and experimental conditions. ZINBA's flexibility…

G T A T C G C T A
ChIPSeq Peak…
Desktop

ChIPSeq Peak Finder

A tool to find peaks from ChIPSeq data generated from the Solexa/Illumina…

A tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform.

G T A T C G C T A
T-PIC
Desktop

T-PIC Tree shape Peak Identification for ChIP-Seq

A software for determining DNA/protein binding sites from a ChIP-Seq experiment.

A software for determining DNA/protein binding sites from a ChIP-Seq experiment.

G T A T C G C T A
HMCan
Desktop

HMCan Histone Modification in Cancer

It is Hidden Markov Model based tool that is developed to detect histone…

It is Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data.

G T A T C G C T A
Sole-Search
Web

Sole-Search

An integrated analysis program for peak detection and functional annotation…

An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Sole-Search (i) converts raw data into a format for visualization on a genome browser, (ii) outputs…

G T A T C G C T A
CASSys
Web

CASSys ChIP-seq data Analysis Software System

An integrated, user-friendly software system, spanning all steps of ChIP-seq…

An integrated, user-friendly software system, spanning all steps of ChIP-seq data analysis. CASSys supersedes the laborious application of several single command line tools. CASSys provides…

Related Websites
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.