biomaRt A bridge from R to BioMart databases - for instance Ensembl
cellHTS2 Analysis of cell-based high-throughput screens
DESeq Testing for differential expression in RNA-Seq and other count data
DEXSeq Inference of differential exon usage in RNA-Seq
EBImage Image processing and analysis toolkit for R
genomeIntervals Operations on genomic intervals such as merging, overlap detection, or computing distances between intervals
HilbertVis Visualize long vectors of data by means of Hilbert curves
imageHTS Analysis of high-throughput microscopy-based screens
rhdf5 HDF5 interface to R
Ringo Analysis of ChIP-chip data
tilingArray Transcript mapping with high-density oligonucleotide tiling arrays
vsn Normalization and variance stabilizing transformation of microarray data.

High-throughput sequencing

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


HilbertVis Visualization of genomic data with the Hilbert curve