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, more than 460 packages, and an active user community.
Bioconductor can import diverse sequence-related file types, including fasta, fastq, ELAND, MAQ, BWA, Bowtie, SSOAP, BAM, gff, bed, and wig files. Packages support common and advanced sequence manipulation operations such as trimming, transformation, and alignment. Domain-specific analyses include quality assessment, ChIP-seq, differential expression, RNA-seq, and other approaches. Bioconductor includes an interface to the Sequence Read Archive (via the SRAdb package).
Bioconductor is open access and available for installation here.