deepTools: a flexible platform for exploring deep-sequencing data

By Fidel Ramírez, F. Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke. Nucleic Acids Res., 2014

3,247 citations recorded by the source corpus.

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6086ffebd5b656b4a08bf971069e1bd1f5b68770

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Citations in the corpus

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (2016, positive): “Binding signals were calculated by deepTools (Ramı́rez et al., 2014), and GO enrichment was calculated by g:Profiler (Reimand et al.”
Complex heatmap visualization (2022, background): “An enriched heatmap specifically visualizes the enrichment of a certain type of genomic signal on a list of genomic features of interest [34].”
FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data (2017, methodology): “For each cell type, reads from all DNase-seq replicates were trimmed down to first nucleotide on the 5’ end, pooled and normalized to lx coverage using deepTools [42],”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, background): “…(13); QIIME for quantitative microbiome analysis from raw DNA sequencing data (14); deepTools for explorative analysis of deeply sequence data (15,16); HiCexplorer (17) for analysis and visualization of Hi-C data; ChemicalToolBox for comprehensive access to cheminformatics libraries and drug…”