limma

Extra Credit builds an outline of limma's docs the first time your work uses it. Until then, start at the official documentation.

• GenomicRanges Representation and manipulation of genomic intervals
• DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets
• SummarizedExperiment A container (S4 class) for matrix-like assays
• BiocParallel Bioconductor facilities for parallel evaluation
• AnnotationDbi Manipulation of SQLite-based annotations in Bioconductor
• zlibbioc An R packaged zlib-1.2.5
• MatrixGenerics S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
• Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
• rtracklayer R interface to genome annotation files and the UCSC genome browser
• biomaRt Interface to BioMart databases (i.e. Ensembl)
• KEGGREST Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
• GenomicAlignments Representation and manipulation of short genomic alignments