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Resource:Bioconductor

Name: Resource:Bioconductor
Description: Tools for the analysis and comprehension of high-throughput genomic data that uses the R statistical programming language, is open source and open development. It has two releases each year, 749 software packages (March 2014), and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).

There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations.

Bioconductor packages the GO ontology into their semi-annual release, with software tools to: query; join with diverse additional gene, microarray, and sequence annotations; incorporate GO into annotation, differential expression, and gene set enrichment work flows; and visualize.

The broad goals of the Bioconductor project are:

  • To provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data.
  • To facilitate the inclusion of biological metadata in the analysis of genomic data, e.g. literature data from PubMed, annotation data from LocusLink.
  • To provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software.
  • To further scientific understanding by producing high-quality documentation and reproducible research.
  • To train researchers on computational and statistical methods for the analysis of genomic data.
Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Other Name(s): Biobonductor - Open Source Software for Bioinformatics
Abbreviation: Bioconductor
Parent Organization: Resource:Fred Hutchinson Cancer Research Center
Supporting Agency: NIH, Resource:Catt Family Foundation, Resource:Dana-Farber Cancer Institute
Grant: #1R33 HG002708
Resource Type(s): Data analysis software
Resource: Resource
URL: http://www.bioconductor.org/
*Id: nif-0000-10445
PMID: PMID 15461798
Publication link: http://genomebiology.com/content/pdf/gb-2004-5-10-r80.pdf
Related to: Resource:Gene Ontology Tools, Resource:GO, Resource:OMICtools
Availability: Open unspecified license, Free for academic use, The community can contribute to this resource
Keywords: Transcription factor, cis-eQTL, eQTL, analysis, genomic, metadata, microarray, statistical, variant, annotation, High throughput assay, Sequence data, Sequence, Flow, Gene, term enrichment, text mining, Genetic, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, software library, statistical analysis, other analysis, Flexible integration of GO into statistical analysis and comprehension of high-throughput genetic data, visualization, high-throughput, genetics, R
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:Bioconductor

Resource:CRCView, Resource:asSeq

Parts of Resource:Bioconductor

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Xref: OMICS_01759

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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:BioconductorRDF feed
AbbrevBioconductor  +
AvailabilityOpen unspecified license  +, Free for academic use  +, and The community can contribute to this resource  +
CommentGO data updates: every three months (or more frequently) / org-id: bioconductor
CurationStatuscurated  +
DefiningCitationhttp://www.bioconductor.org/  +
DefinitionTools for the analysis and comprehension o Tools for the analysis and comprehension of high-throughput genomic data that uses the R statistical programming language, is open source and open development. It has two releases each year, 749 software packages (March 2014), and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).

There is also a development version, to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations. Bioconductor packages the GO ontology into their semi-annual release, with software tools to: query; join with diverse additional gene, microarray, and sequence annotations; incorporate GO into annotation, differential expression, and gene set enrichment work flows; and visualize. The broad goals of the Bioconductor project are:

  • To provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data.
  • To facilitate the inclusion of biological metadata in the analysis of genomic data, e.g. literature data from PubMed, annotation data from LocusLink.
  • To provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software.
  • To further scientific understanding by producing high-quality documentation and reproducible research.
  • To train researchers on computational and statistical methods for the analysis of genomic data.
Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
patible, Linux compatible, Unix compatible
ExampleImageBioconductor.PNG  +
GrantCategory:#1R33 HG002708   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleData analysis software  +
Idnif-0000-10445  +
Is part ofResource:Fred Hutchinson Cancer Research Center  +
KeywordsTranscription factor  +, Cis-eQTL  +, EQTL  +, Analysis  +, Genomic  +, Metadata  +, Microarray  +, Statistical  +, Variant  +, Annotation  +, High throughput assay  +, Sequence data  +, Sequence  +, Flow  +, Gene  +, Term enrichment  +, Text mining  +, Genetic  +, Ontology or annotation browser  +, Ontology or annotation search engine  +, Ontology or annotation visualization  +, Database or data warehouse  +, Software library  +, Statistical analysis  +, Other analysis  +, Flexible integration of GO into statistical analysis and comprehension of high-throughput genetic data  +, Visualization  +, High-throughput  +, Genetics  +, and R  +
LabelResource:Bioconductor  +
ModifiedDate29 July 2014  +
PMID15461798  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://genomebiology.com/content/pdf/gb-2004-5-10-r80.pdf  +
RelatedToResource:Gene Ontology Tools  +, Resource:GO  +, and Resource:OMICtools  +
SuperCategoryResource  +
Supporting AgencyNational Institutes of Health  +, Resource:Catt Family Foundation  +, and Resource:Dana-Farber Cancer Institute  +
SynonymBiobonductor - Open Source Software for Bioinformatics  +
TwitterBioconductor  +
XrefResource:Bioconductor  +