deepTools: a flexible platform for exploring deep-sequencing data
Open accessAbstract
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.
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GC-bias in ChIP-seq was estimated and corrected using input chromatin.
“GC-bias was estimated for input chromatin samples using computeGCBias (Benjamini and Speed, 2012) from deepTools (Ramírez et al., 2014).”
From SALL4 controls cell fate in response to DNA base composition (2021) · cites this paper as Ramírez et al., 2014
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- Authors
- Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A., & Manke, T.
- Affiliations
- Max Planck Institute of Immunobiology and Epigenetics (DE)
- University of Freiburg (DE)
- Corresponding author
- Manke, Thomas
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-05-05
- Volume
- 42
- Issue
- W1
- Pages
- W187-W191
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4086134
- OpenAlex
- W2158789637
- Cited by
- 3,738
- References
- 0
- Citations by year
- 2026: 456 · 2025: 556 · 2024: 611 · 2023: 479 · 2022: 391 · 2021: 373 · 2020: 292 · 2019: 205 · 2018: 142 · 2017: 131 · 2016: 67 · 2015: 24 · 2014: 11
- FWCI
- 31.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion)
- Figshare (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Figshare (cc-by)
- Funders
- Deutsche Forschungsgemeinschaft (SFB 992)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- read mapping, heatmaps, data visualization, open-source bioinformatics software, reproducible analysis
- MeSH terms
- Computer Graphics, Software, Internet, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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