The basic idea of latent semantic analysis (LSA) is, 
  that text do have a higher order (=latent semantic) structure which, 
  however, is obscured by word usage (e.g. through the use of synonyms 
  or polysemy). By using conceptual indices that are derived statistically 
  via a truncated singular value decomposition (a two-mode factor analysis) 
  over a given document-term matrix, this variability problem can be overcome.

Foundation of external vector representation and manipulation in
Bioconductor

Provides memory efficient S4 classes for storing sequences
	"externally" (e.g. behind an R external pointer, or on disk).

methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors,
IRanges

io-utils.R RDS-random-access.R SharedVector-class.R
SharedRaw-class.R SharedInteger-class.R SharedDouble-class.R
XVector-class.R XRaw-class.R XInteger-class.R XDouble-class.R
XVectorList-class.R XRawList-class.R XRawList-comparison.R
XIntegerViews-class.R XDoubleViews-class.R OnDiskRaw-class.R
RdaCollection-class.R RdsCollection-class.R
intra-range-methods.R compact-methods.R reverse-methods.R
slice-methods.R view-summarization-methods.R
updateObject-methods.R zzz.R

Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic
	annotations and alignments is playing a central role when it comes
	to analyzing high-throughput sequencing data (a.k.a. NGS data).
	The GenomicRanges package defines general purpose containers for
	storing and manipulating genomic intervals and variables defined along
	a genome. More specialized containers for representing and manipulating
	short alignments against a reference genome, or a matrix-like
	summarization of an experiment, are defined in the GenomicAlignments
	and SummarizedExperiment packages, respectively. Both packages build
	on top of the GenomicRanges infrastructure.

Genetics, Infrastructure, DataRepresentation, Sequencing,
Annotation, GenomeAnnotation, Coverage

Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
BiocStyle