easyRNASeq

http://bioconductor.org/packages/2.12/bioc/vignettes/easyRNASeq/inst/doc/easyRNASeq.pdf

This file describes the use of the easyRNASeq package to ease the processing
of RNA-seq data in R/Bioconductor. RNA-seq [Mortazavi et al., 2008] was
introduced as a new method to perform Gene Expression Analysis, using the
advantages of the high throughput of Next-Generation Sequencing (NGS)
machines.

The goal of this vignette is, first, to show an example of the easyRNASeq
function that generates a count table for the selected genic features of inter-
est, i.e. exons, transcripts, gene models, etc. using the read data and the
genic and genomic annotations. This overall process is described in figure 1,
page 5. Shortly, the genomic and genic annotation will be retrieved from the
selected/preferred source and converted into an appropriate object. In par-
allel, the sequenced reads' information (e.g. chromosome, position, strand,
etc.) will be retrieved from the alignment file and, similarly, converted to
an appropriate object. Then, the reads contained in the reads object are
summarized per genic annotation contained in the annotation object, which
give raise to a count table that, finally, can be normalized using additional
R packages.