The Short Read Analysis Toolkit contains a number of useful tools to analyze data from ChIP-Seq and other experiments producing short sequence reads.
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Vancouver Short Read Analysis Package
This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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