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String manipulations, efficient matching, and alignments using Biostrings

An introduction to the Biostrings/BSgenome framework (pdf)
Biostrings/BSgenome Lab (pdf)
Biostrings/BSgenome Lab (R script with solutions)
Sequence Alignment of Short Read Data using Biostrings (pdf)
Sequence Alignment of Short Read Data using Biostrings (R script)
topReads.rda (R data file)