DESeq Testing for differential expression in RNA-Seq and other count data
genomeIntervals Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals
mgsa Model-based Gene Set Analysis(MGSA), a Bayesian modelling approach for gene set enrichment

High-throughput sequencing

HTSeq A Python package for processing and analysing data from high-throughput sequencing assays

Sequence Analysis

BLAST SK1/ YJM789/S288c BLAST server for assembled genomes from S. cerevisiae strains SK1, YJM789, and S288c