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Differential peak calling software tools | ChIP sequencing data analysis

Increasing number of ChIP-seq experiments are investigating transcription factor binding under multiple experimental conditions, for example, various treatment conditions, several distinct time points and different treatment dosage levels. Hence,…
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DiffBind
Desktop

DiffBind

Provides functions for processing ChIP-seq data enriched for genomic loci where…

Provides functions for processing ChIP-seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-seq peak callers and aligned sequence read…

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MAnorm
Desktop

MAnorm

A simple and effective method for quantitative comparison of ChIP-Seq data sets…

A simple and effective method for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences…

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csaw
Desktop

csaw

Provides a framework for the de novo detection of differentially bound genomic…

Provides a framework for the de novo detection of differentially bound genomic regions. csaw uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical…

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DBChIP
Desktop

DBChIP

Detects differential binding in a quantitatively principled way by formally…

Detects differential binding in a quantitatively principled way by formally testing hypothesis of non-differential binding at each putative binding site. DBChIP assigns uncertainty measure (P-values)…

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BEADS
Desktop

BEADS Bias Elimination Algorithm for Deep Sequencing

A normalization scheme that corrects nucleotide composition bias, mappability…

A normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

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diffReps
Desktop

diffReps

A program to detect differential sites from two comparison groups of ChIP-seq…

A program to detect differential sites from two comparison groups of ChIP-seq samples. diffReps is independent of any peak calling program and provides several statistical tests to take advantage of…

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DIME
Desktop

DIME Differential Identification using Mixtures Ensemble

A package for identification of biologically significant differential binding…

A package for identification of biologically significant differential binding sites between two conditions using ChIP-seq data. DIME considers a collection of finite mixture models combined with a…

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HMCan-diff
Desktop

HMCan-diff

Aims to detect differences in histone mark profiles between samples with…

Aims to detect differences in histone mark profiles between samples with significant genomic discrepancies. HMCan-diff is designed to analyze ChIP-seq data to detect changes in histone modifications…

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ChIPDiff…
Desktop

ChIPDiff Library Comparison

Provides a solution for the identification of Differential Histone Modification…

Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2).

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MMDiff
Desktop

MMDiff

This package detects statistically significant difference between read…

This package detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples.

THOR
Desktop

THOR

An HMM-based approach to detect and analyze differential peaks in two sets of…

An HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, normalization…

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GenoGAM
Desktop

GenoGAM Genome-wide Generalized Additive Model

Brings the well-established and flexible generalized additive models framework…

Brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. GenoGAM provides significance testing for differential…

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POLYPHEMUS
Desktop

POLYPHEMUS

Integrates read-count signal intensity profiles with RNA Polymerase II binding…

Integrates read-count signal intensity profiles with RNA Polymerase II binding site annotations to identify coding regions associated with potential transcriptional activity. Furthermore, POLYPHEMUS…

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normR
Desktop

normR normR obeys regime mixture rules

A tool for normalization and difference calling in ChIP-seq data. normR…

A tool for normalization and difference calling in ChIP-seq data. normR performs normalization and difference calling simultaneously to identify genomic regions enriched by the ChIP-procedure. In…

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chromstaR
Desktop

chromstaR

An algorithm for the computational inference of combinatorial chromatin state…

An algorithm for the computational inference of combinatorial chromatin state dynamics across an arbitrary number of conditions. ChromstaR uses a multivariate Hidden Markov Model to determine the…

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ChIPComp
Desktop

ChIPComp

A statistical method to perform quantitative comparison of multiple ChIP-seq…

A statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. Simulations and real…

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EpiCenter
Desktop

EpiCenter

A powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting…

A powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications (histone acetylation/methylation…

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ODIN
Desktop

ODIN

An HMM-based approach to detect and analyse differential peaks in pairs of…

An HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework.

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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…

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histoneHMM
Desktop

histoneHMM

A software tool to analyse ChIP-seq data of histone modifications with broad…

A software tool to analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. histoneHMM allows for calling modified regions in single samples as well as for calling…

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ImpulseDE2
Desktop

ImpulseDE2

Corrects batch effects (from multiple confounding variables) and library depth.…

Corrects batch effects (from multiple confounding variables) and library depth. ImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing…

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QChIPat
Desktop

QChIPat

A quantitative method for comparing two biological ChIP-seq samples. The method…

A quantitative method for comparing two biological ChIP-seq samples. The method employs a new global normalization method: nonparametric empirical Bayes (NEB) correction normalization, utilizes…

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