The Genomic HyperBrowser: inferential genomics at the sequence level

@article{Sandve2010TheGH,
  title={The Genomic HyperBrowser: inferential genomics at the sequence level},
  author={Geir Kjetil Sandve and Sveinung Gundersen and Halfdan Rydbeck and Ingrid Kristine Glad and Lars Holden and Marit Holden and Knut Liest{\o}l and Trevor Clancy and Egil Ferkingstad and Morten Johansen and Vegard Nygaard and Eivind T{\o}stesen and Arnoldo Frigessi and Eivind Hovig},
  journal={Genome Biology},
  year={2010},
  volume={11},
  pages={R121 - R121}
}
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the… 
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94 Citations
Highly Influential Citations
16
Background Citations
21
Methods Citations
46
Results Citations
1

94 Citations

The Genomic HyperBrowser: an analysis web server for genome-scale data

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GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome

GSuite HyperBrowser is the first comprehensive solution for integrative analysis of dataset collections across the genome and epigenome, an open-source system for streamlined acquisition and customizable statistical analysis of large collections of genome-wide datasets.

Retrieval of Genomic Data using PyTables

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EpiExplorer: live exploration and global analysis of large epigenomic datasets

EpiExplorer is described, a web tool for exploring genome and epigenome data on a genomic scale and its utility is demonstrated by describing a hypothesis-generating analysis of DNA hydroxymethylation in relation to public reference maps of the human epigenome.

Supplemental material for ” The differential disease regulome ”

An abstract representation of generic genomic elements by means of mathematical objects is constructed, which the biologist can explore advanced and problem-specific null hypotheses, hierarchically preserving various degrees of track information, strengthening power and reducing false discoveries.

Introduction Online Resources for Genomic Analysis Using High-Throughput Sequencing

The use and applications of common file formats for coding and storing genomic data are described and several web-accessible open-source resources for the visualization and analysis of NGS data are considered.

Epigenomic annotation‐based interpretation of genomic data: from enrichment analysis to machine learning

The hierarchy of tools and methods reviewed here presents a practical guide for the interpretation of genome‐wide ROIs within an epigenomic context and discusses leading tools and machine learning methods utilizing epigenomic and 3D genome structure data.

Recommendations for the FAIRification of genomic track metadata

A first iteration of a draft standard for genomic track metadata, as well as the accompanying software ecosystem, can be adapted or extended to future needs of the research community regarding data, methods and tools, balancing the requirements of both data submitters and analytical end-users.

Online resources for genomic analysis using high-throughput sequencing.

The use and applications of common file formats for coding and storing genomic data are described and several web-accessible open-source resources for the visualization and analysis of NGS data are considered.

Cogito: automated and generic comparison of annotated genomic intervals

Cogito implements a novel approach to facilitate high-level overview analyses of complex datasets, and offers additional insights into the data without the need for a full, time-consuming reanalysis.
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