Cargando…

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

BACKGROUND: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these pu...

Descripción completa

Detalles Bibliográficos
Autores principales:	Simovski, Boris, Vodák, Daniel, Gundersen, Sveinung, Domanska, Diana, Azab, Abdulrahman, Holden, Lars, Holden, Marit, Grytten, Ivar, Rand, Knut, Drabløs, Finn, Johansen, Morten, Mora, Antonio, Lund-Andersen, Christin, Fromm, Bastian, Eskeland, Ragnhild, Gabrielsen, Odd Stokke, Ferkingstad, Egil, Nakken, Sigve, Bengtsen, Mads, Nederbragt, Alexander Johan, Thorarensen, Hildur Sif, Akse, Johannes Andreas, Glad, Ingrid, Hovig, Eivind, Sandve, Geir Kjetil
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Technical Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493745/ https://www.ncbi.nlm.nih.gov/pubmed/28459977 http://dx.doi.org/10.1093/gigascience/gix032

Ejemplares similares

hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks
por: Kalyanasundaram, Sumana, et al.
Publicado: (2023)

The Genomic HyperBrowser: inferential genomics at the sequence level
por: Sandve, Geir K, et al.
Publicado: (2010)

The Genomic HyperBrowser: an analysis web server for genome-scale data
por: Sandve, Geir K., et al.
Publicado: (2013)

c-Myb Binding Sites in Haematopoietic Chromatin Landscapes
por: Bengtsen, Mads, et al.
Publicado: (2015)

The differential disease regulome
por: Sandve, Geir K, et al.
Publicado: (2011)

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets
por: Rydbeck, Halfdan, et al.
Publicado: (2015)

In the loop: promoter–enhancer interactions and bioinformatics
por: Mora, Antonio, et al.
Publicado: (2016)

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
por: Grytten, Ivar, et al.
Publicado: (2019)

Coordinates and intervals in graph-based reference genomes
por: Rand, Knut D., et al.
Publicado: (2017)

The rainfall plot: its motivation, characteristics and pitfalls
por: Domanska, Diana, et al.
Publicado: (2017)

Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
por: Paulsen, Jonas, et al.
Publicado: (2013)

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis
por: Domanska, Diana, et al.
Publicado: (2018)

Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
por: Grytten, Ivar, et al.
Publicado: (2020)

Personal Cancer Genome Reporter: variant interpretation report for precision oncology
por: Nakken, Sigve, et al.
Publicado: (2018)

Galaxy Portal: interacting with the galaxy platform through mobile devices
por: Børnich, Claus, et al.
Publicado: (2016)

Genome build information is an essential part of genomic track files
por: Kanduri, Chakravarthi, et al.
Publicado: (2017)

Colocalization analyses of genomic elements: approaches, recommendations and challenges
por: Kanduri, Chakravarthi, et al.
Publicado: (2019)

Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
por: Lemma, Roza B., et al.
Publicado: (2021)

Identifying elemental genomic track types and representing them uniformly
por: Gundersen, Sveinung, et al.
Publicado: (2011)

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
por: Paulsen, Jonas, et al.
Publicado: (2014)

MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape
por: Lemma, Roza Berhanu, et al.
Publicado: (2023)

Chromosomal instability and a deregulated cell cycle are intrinsic features of high‐risk gastrointestinal stromal tumours with a metastatic potential
por: Namløs, Heidi Maria, et al.
Publicado: (2023)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
por: Simovski, Boris, et al.
Publicado: (2018)

Sequential Monte Carlo multiple testing
por: Sandve, Geir Kjetil, et al.
Publicado: (2011)

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
por: Paulsen, Jonas, et al.
Publicado: (2014)

Sample-Index Misassignment Impacts Tumour Exome Sequencing
por: Vodák, Daniel, et al.
Publicado: (2018)

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers
por: Lemma, Roza Berhanu, et al.
Publicado: (2022)

A survey of motif discovery methods in an integrated framework
por: Sandve, Geir Kjetil, et al.
Publicado: (2006)

Patterns of genomic evolution in advanced melanoma
por: Birkeland, E., et al.
Publicado: (2018)

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
por: Grytten, Ivar, et al.
Publicado: (2022)

Gene Dosage, Expression, and Ontology Analysis Identifies Driver Genes in the Carcinogenesis and Chemoradioresistance of Cervical Cancer
por: Lando, Malin, et al.
Publicado: (2009)

Compo: composite motif discovery using discrete models
por: Sandve, Geir Kjetil, et al.
Publicado: (2008)

The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
por: Nakken, Sigve, et al.
Publicado: (2009)

Recommendations for the FAIRification of genomic track metadata
por: Gundersen, Sveinung, et al.
Publicado: (2021)

Identification of genetic variants for clinical management of familial colorectal tumors
por: Dominguez-Valentin, Mev, et al.
Publicado: (2018)

Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains
por: Gabrielsen, C., et al.
Publicado: (2015)

NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
por: Khelik, Ksenia, et al.
Publicado: (2020)

Mutational analysis and protein profiling predict drug sensitivity in multiple myeloma cell lines
por: Giliberto, Mariaserena, et al.
Publicado: (2022)

Improved benchmarks for computational motif discovery
por: Sandve, Geir Kjetil, et al.
Publicado: (2007)

Ten simple rules for quick and dirty scientific programming
por: Balaban, Gabriel, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_f5n6n2t5g8j6ocaun74s15297l