About
Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 554 software packages, and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).

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Use Bioconductor for...

• Microarrays

  Import Affymetrix, Illumina, Nimblegen, Agilent, and other platforms. Perform quality assessment, normalization, differential expression, clustering, classification, gene set enrichment, genetical genomics and other workflows for expression, exon, copy number, SNP, methylation and other assays. Access GEO, ArrayExpress, Biomart, UCSC, and other community resources.

• Variants

  Read and write VCF files. Identify structural location of variants and compute amino acid coding changes for non-synonymous variants. Use SIFT and PolyPhen database packages to predict consequence of amino acid coding changes.

• Sequence Data

  Import fasta, fastq, ELAND, MAQ, BWA, Bowtie, BAM, gff, bed, wig, and other sequence formats. Trim, transform, align, and manipulate sequences. Perform quality assessment, ChIP-seq, differential expression, RNA-seq, and other workflows. Access the Sequence Read Archive.

• Annotation

  Use microarray probe, gene, pathway, gene ontology, homology and other annotations. Access GO, KEGG, NCBI, Biomart, UCSC, vendor, and other sources.

• High Throughput Assays

  Import, transform, edit, analyze and visualize flow cytometric, mass spec, HTqPCR, cell-based, and other assays.