DESeqTesting for differential expression in RNA-Seq and other count data
easyRNASeqCount summarisation and normalisation for RNA-Seq data
genomeIntervalsOperations on genomic intervals such as merging, overlap detection, or computing distances between intervals
mgsaModel-based Gene Set Analysis(MGSA), a Bayesian modelling approach for gene set enrichment

High-throughput sequencing

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

Sequence Analysis

BLAST SK1/ YJM789/S288cBLAST server for assembled genomes from S. cerevisiae strains SK1, YJM789, and S288c