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Data visualization software tools | ChIP sequencing data analysis

UCSC Genome Browser
Web

UCSC Genome Browser University of California Santa Cruz Genome Browser

Displays the assembled human genome and other mammalian genomes. UCSC Genome…

Displays the assembled human genome and other mammalian genomes. UCSC Genome Browser provides browsers for more than 180 assemblies and over 100 species. It provides a collection of tools to explore…

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MSR
Desktop

MSR

A multiscale framework to analyze and visualize the information content of…

A multiscale framework to analyze and visualize the information content of genomic signals.

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genomation
Desktop

genomation

An R package that contains a collection of tools for visualizing and analyzing…

An R package that contains a collection of tools for visualizing and analyzing genome-wide data sets. The package works with a variety of genomic interval file types and enables easy summarization…

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SNPhood
Desktop

SNPhood

A user-friendly Bioconductor R package to investigate, quantify and visualise…

A user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or transcription factor binding sites…

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VAP
Desktop

VAP Versatile Aggregate Profiler

Designed to be used by experimental and computational biologists to generate…

Designed to be used by experimental and computational biologists to generate profiles of genomic datasets over groups of regions of interest, using either an absolute or a relative method.

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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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BioWardrobe
Desktop
Web

BioWardrobe

Allows users to store, visualize and analyze epigenomics and transcriptomics…

Allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow…

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VOE
Desktop
Mobile
Web

VOE Visual Omics Explorer

A cross-platform data visualization portal that is implemented using only HTML…

A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the…

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dictyExpress
Web

dictyExpress

Enables the broad adoption of next generation sequencing (NGS) based inquiries.…

Enables the broad adoption of next generation sequencing (NGS) based inquiries. dictyExpress is a web application designed for exploration of transcriptomics datasets. It allows users to select among…

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agplus
Desktop

agplus

Aggregation plots are frequently used to evaluate signal distributions at…

Aggregation plots are frequently used to evaluate signal distributions at user-interested points in ChIP-Seq data analysis. agplus enables rapid and flexible generation of text tables tailored for…

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MicroScope
Web
Desktop

MicroScope

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic…

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic data, including features to support differential expression analysis, heatmap production, principal component, gene…

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fluff
Desktop

fluff

A software package that allows for simple exploration, clustering and…

A software package that allows for simple exploration, clustering and visualization of high-throughput sequencing experiments. fluff contains three command-line tools to generate publication-quality…

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ColoWeb
Web

ColoWeb

A web-based service for evaluating the colocation of genomic features. Users…

A web-based service for evaluating the colocation of genomic features. Users submit genomic regions of interest, for example, a set of locations from a ChIP-seq analysis. ColoWeb compares the…

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SPARTA
Desktop

SPARTA

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a…

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists…

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PAVIS
Web

PAVIS Peak Annotation and VISualization

Allows to annotate and visualize ChIP-seq peak data. PAVIS is a web-based tool…

Allows to annotate and visualize ChIP-seq peak data. PAVIS is a web-based tool designed and developed for ease of use for biologists or bench scientists. The software offers two primary functions:…

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SraTailor
Desktop

SraTailor

A simple GUI software tool for visualizing published ChIP-seq raw data.…

A simple GUI software tool for visualizing published ChIP-seq raw data. SraTailor automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of…

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Podbat
Desktop

Podbat POsitioning DataBase and Analysis Tool

Allows to visualize, analyze and store genomic positioning data. Podbat is an…

Allows to visualize, analyze and store genomic positioning data. Podbat is an integrated computational tool develop for use on epigenomics datasets. The software follows a simple flowchart and…

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D-peaks
Web

D-peaks

Plots the short reads binding profiles of a ChIP-seq experiment. D-peaks is a a…

Plots the short reads binding profiles of a ChIP-seq experiment. D-peaks is a a ChIP-seq result analysis tool which draws a precise representation of several ChIP-seq experiments along the genomes in…

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Heatmaps
Desktop

Heatmaps

Provides a flexible way to plot genome-wide data in many forms. Heatmaps is a…

Provides a flexible way to plot genome-wide data in many forms. Heatmaps is a software which provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq…

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ChIPMonk
Desktop

ChIPMonk

A tool to visualise and analyse ChIP-on-chip array data.

A tool to visualise and analyse ChIP-on-chip array data.

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