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Bioconductor

Bioconductor

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.

 Bioconductor 3.0

Price
Free to download

Size
-
License

Artistic License 2.0

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

Website
www.bioconductor.org

System Requirements
Uses biocLite.R script to install

Support:
Manual, FAQ, Introduction to R and Bioconductor (PDF), Mailing Lists

Selected Reviews:

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

Return to Bioinformatics Tools Home Page

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Last Updated Friday, July 03 2015 @ 06:03 AM EDT


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