deepTools2: a next generation web server for deep-sequencing data analysis
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Summary
An update to the Galaxy-based web server deepTools, which allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches, is presented.
- Type
- article
- Published
- 2016-04-13
- Cited by
- 6,979
- References
- 20
- Access
- Open access
- OpenAlex
- https://openalex.org/W2341539131
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3719347
Keywords
Visualization, Suite, Web server, Workflow, Computer science
References
- Using Galaxy to Perform Large‐Scale Interactive Data Analyses
- Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
- ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
- Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing
- Integrative analysis of 111 reference human epigenomes
- Identifying ChIP-seq enrichment using MACS
- Dissemination of scientific software with Galaxy ToolShed
- The Sequence Alignment/Map format and SAMtools
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Droplet barcoding for single cell transcriptomics applied to embryonic stem cells
- Systematic evaluation of factors influencing ChIP-seq fidelity
- Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4.
- An Interactive Analysis and Exploration Tool for Epigenomic Data
- Genomation: a Toolkit to Summarize, Annotate and Visualize Genomic Intervals
- deepTools: a flexible platform for exploring deep-sequencing data
- High-affinity sites form an interaction network to facilitate spreading of the MSL complex across the X chromosome in Drosophila
- The UCSC Genome Browser database: 2016 update
- An Integrated Encyclopedia of DNA Elements in the Human Genome
- Using Galaxy to Perform Large-Scale Interactive Data Analyses
- An integrated encyclopedia of DNA elements in the human genome
Cited by
- Reprogramming of the histone H3.3 landscape in the early mouse embryo
- Aberrant activation of a gastrointestinal transcriptional circuit in prostate cancer mediates castration resistance
- Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants
- A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
- Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome
- Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
- Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
- GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
- RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
- normR: Regime enrichment calling for ChIP-seq data
- Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
- CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells
- CTCF and cohesin regulate chromatin loop stability with distinct dynamics
- CENP-A associated lncRNAs influence chromosome segregation in human cells
- O-Linked N-Acetylglucosamine (O-GlcNAc) Expression Levels Epigenetically Regulate Colon Cancer Tumorigenesis by Affecting the Cancer Stem Cell Compartment via Modulating Expression of Transcriptional Factor MYBL1*
- The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses
- The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression
- Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells
- Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria
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