Bioconductor

biomaRtA bridge from R to BioMart databases - for instance Ensembl
cellHTS2Analysis of cell-based high-throughput screens
DESeqTesting for differential expression in RNA-Seq and other count data
DEXSeqInference of differential exon usage in RNA-Seq
EBImageImage processing and analysis toolkit for R
genomeIntervalsOperations on genomic intervals such as merging, overlap detection, or computing distances between intervals
HilbertVisVisualize long vectors of data by means of Hilbert curves
imageHTSAnalysis of high-throughput microscopy-based screens
rhdf5HDF5 interface to R
RingoAnalysis of ChIP-chip data
tilingArrayTranscript mapping with high-density oligonucleotide tiling arrays
vsnNormalization and variance stabilizing transformation of microarray data.

High-throughput sequencing

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

Visualisation

HilbertVisVisualization of genomic data with the Hilbert curve