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Bioconductor

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.

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.

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.

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

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

Find candidate binding sites for known transcription factors via sequence matching.

Explore material from recent courses, including Intermediate R / Bioconductor for High Throughput Sequence Analysis (February 14-15, 2013).