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Peak annotation

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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…

CEAS
Desktop
Web

CEAS Cis-regulatory Element Annotation System

A software tool designed to characterize genome-wide protein-DNA interaction…

A software tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. CEAS provides summary statistics on ChIP enrichment in important genomic…

ChIPpeakAnno
Desktop

ChIPpeakAnno

Facilitates batch annotation of enriched peaks identified from ChIP-seq,…

Facilitates batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions.…

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UROPA
Desktop

UROPA Universal RObust Peak Annotator

Allows to annotate peaks or other genomic regions. UROPA permits linkage of…

Allows to annotate peaks or other genomic regions. UROPA permits linkage of individual queries including prioritization. It can parse custom generated GTF files with arbitrary keywords. The tool can…

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FunChIP
Desktop

FunChIP

Classifies peaks with a functional analysis of their shapes. FunChIP is an R…

Classifies peaks with a functional analysis of their shapes. FunChIP is an R package which consists in a series of methods for the GenomicRanges class, which sequentially add metadata columns to the…

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ChIPseeker
Desktop

ChIPseeker

Annotates ChIP-seq data analysis. ChIPseeker supports annotating ChIP peaks and…

Annotates ChIP-seq data analysis. ChIPseeker supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions.…

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PeakAnnotator
Desktop

PeakAnnotator

Assist in annotation of genome-wide signal enrichment peaks derived from…

Assist in annotation of genome-wide signal enrichment peaks derived from experimental results. PeakAnnotator couples a modified version of the nested containment list (NCList) algorithm to a binary…

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PeakAnalyzer
Desktop

PeakAnalyzer

Allows users to process genomic loci with an emphasis on datasets consisting of…

Allows users to process genomic loci with an emphasis on datasets consisting of ChIP-derived signal peaks. PeakAnalyzer is an open source software composed of two main functions: (i) PeakSplitter…

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PAPST
Desktop

PAPST Peak Assignment and Profile Search Tool

A user friendly program for analysis of ChIP-Seq experiments. PAPST allows…

A user friendly program for analysis of ChIP-Seq experiments. PAPST allows users to interact with the significant peaks called from ChIP-seq experiments. It allows powerful co-localization analysis…

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annotatr
Desktop

annotatr

An R package to easily and quickly summarize, and visualize the association of…

An R package to easily and quickly summarize, and visualize the association of genomic regions with genomic annotations. The annotatr package reports all intersections of regions and annotations,…

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AnnotateGenomic…
Web

AnnotateGenomicRegions

A web-application that allows researchers with a wide range of bioinformatics…

A web-application that allows researchers with a wide range of bioinformatics skills to annotate genomic regions of interest, e.g. ChIP-seq peaks, with overlapping or neighboring annotations. In…

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annoPeak
Web

annoPeak

Helps to annotate binding sites and compare binding profiles from multiple…

Helps to annotate binding sites and compare binding profiles from multiple experiments. annoPeak is a web application that includes analytical tools to identify and illustrate binding profiles…

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