Bioconductor – tools for the analysis and comprehension of high-throughput genomic data

Bioconductor is a free, open source and open development software project which provides tools for the analysis and comprehension of high-throughput genomic data.

Bioconductor uses the statistical R programming language, but does contain contributions in other programming languages.

The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results.

Features include:

  • Provides access to powerful statistical and graphical methods for the analysis of genomic data. Analysis packages address workflows for analysis of:
    • Oligonucleotide arrays.
    • Sequence analysis.
    • Flow cytometry.
    • Other high-throughput genomic data.
  • Each Bioconductor package contains one or more vignettes, documents that provide a textual, task-oriented description of the package’s functionality.
  • Provides software for associating microarray and other genomic data in real time with biological metadata from web databases such as GenBank, Entrez genes and PubMed.
  • Analysis of differentially expressed genes:
    • LIMMA.
      • cDNA Arrays.
      • Affy Arrays.
    • RankProd.
    • SAM.
    • R/maanova.
    • Digital Gene Expression.
  • Dual Color Array packages.
  • Gene Ontologies:
    • General.
    • GOHyperGAII.
    • GSEA.
      GoTools and goCluster.
  • KEGG pathway analysis.
  • Motif identification in promoter regions.
  • Protein structure analysis.
  • MS data analysis.
  • Genome-Wide Association Studies (GWAS).
  • Uses R to add a raft of functionality.

Developer: Vince Carey, Marc Carlson, Sean Davis, Robert Gentleman, Nishant Gopalakrishnan, Wolfgang Huber and many others
License: Artistic License 2.0

Bioconductor is written in R. Learn R with our recommended free books and free tutorials.

Return to Bioinformatics Tools

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