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Tag density plot visualization software tools | ChIP sequencing data analysis

Tag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region.Source text:(Kim et al., 2015) iTagPlot: an accurate computation and interactive…
G T A T C G C T A
ngs.plot
Desktop

ngs.plot

Allows you to easily visualize your next-generation sequencing (NGS) samples at…

Allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. ngs.plot is a useful tool to help fill the gap between massive datasets and genomic…

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…

G T A T C G C T A
Repitools
Desktop

Repitools

A software package for the analysis of enrichment-based epigenomic data.…

A software package for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context,…

G T A T C G C T A
Cistrome
Web

Cistrome

A web-based application called Cistrome, based on the Galaxy open source…

A web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major…

G T A T C G C T A
seqMINER
Desktop

seqMINER

Allows comparison and integration of multiple ChIP-seq datasets and extraction…

Allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. seqMINER can handle the biological complexity of most experimental…

G T A T C G C T A
Spark
Desktop

Spark

A clustering and visualization tool that enables the interactive exploration of…

A clustering and visualization tool that enables the interactive exploration of genome-wide data. It is intended to "spark" insights into genome-scale data sets. The approach utilizes data…

G T A T C G C T A
iTagPlot
Desktop

iTagPlot

Computes tag density across functional features in parallel using multicores…

Computes tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. iTagPlot allows you to stratify features…

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SeqPlots
Desktop

SeqPlots

Visualizes next-generation sequencing (NGS) signals and sequence motif…

Visualizes next-generation sequencing (NGS) signals and sequence motif densities along genomic features using average plots and heatmaps. It can also calculate sequence motif density profiles from…

G T A T C G C T A
metaseq
Desktop

metaseq

A Python library designed to analyze and visualize data from disparate file…

A Python library designed to analyze and visualize data from disparate file formats and experimental protocols (ChIP-seq, RNA-seq, RNA immunoprecipitation and sequencing (RIP-seq), etc.) in a…

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HTSeq
Desktop

HTSeq

A Python library to facilitate the rapid development of scripts. HTSeq offers…

A Python library to facilitate the rapid development of scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates,…

G T A T C G C T A
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…

G T A T C G C T A
TransView
Desktop

TransView

Allows user to create, reach and visualize read densities of sequencing based…

Allows user to create, reach and visualize read densities of sequencing based data sets like ChIP-Seq and RNA-Seq.

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