Hi,

The main option in R is currently easyRNASeq
http://www.bioconductor.org/packages/devel/bioc/html/easyRNASeq.html which
is a front-end to DESeq (or edgeR), two of the most popular RNASeq
packages. This is especially helpful for comparing samples with each other
and handling replicates.

If you've run tophat, you could use cuffdiff / cufflinks to get normalized
transcript counts, as well (but this is not related to R/Bioconductor).

Best,

Kemal

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