deepTools2: a next generation web server for deep-sequencing data analysis

Abstract

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.

Keywords

VisualizationSuiteWeb serverWorkflowComputer scienceSet (abstract data type)OS XWeb serviceCluster analysisWeb applicationWorld Wide WebThe InternetDatabaseOperating systemSoftwareData miningProgramming language

Affiliated Institutions

Related Publications

HMMER web server: 2018 update

Simon Potter , Aurélien Luciani , Sean R. Eddy +3 more

The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov mod...

2018 Nucleic Acids Research 2535 citations

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan , Dannon Baker , Bérénice Batut +17 more

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists acros...

2018 Nucleic Acids Research 3703 citations

Deciphering key features in protein structures with the new ENDscript server

Xavier Robert , Patrice Gouet

ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major...

2014 Nucleic Acids Research 6907 citations

Ensembl 2015

Fiona Cunningham , M Ridwan Amode , Daniel Barrell +46 more

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model orga...

2014 Nucleic Acids Research 1150 citations

The HDOCK server for integrated protein–protein docking

Yumeng Yan , Huanyu Tao , Jiahua He +1 more

The HDOCK server (http://hdock.phys.hust.edu.cn/) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biologi...

2020 Nature Protocols 1546 citations

Publication Info

Year: 2016
Type: article
Volume: 44
Issue: W1
Pages: W160-W165
Citations: 8157
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

deepTools2: a next generation web server for deep-sequencing data analysis

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

8157

OpenAlex

Cite This

APA Style

                            
                                
                                    Fidel Ramírez, 
                                
                                    Devon Ryan, 
                                
                                    Björn Grüning
                                
                                et al.
                            
                            (2016). 
                            deepTools2: a next generation web server for deep-sequencing data analysis. 
                            Nucleic Acids Research
                            , 44
                            (W1)
                            , W160-W165.
                            https://doi.org/10.1093/nar/gkw257
                        

Identifiers

DOI: 10.1093/nar/gkw257