R package to annotate and explore effect of biases in RNA Seq

Question

[User 7754]

I was wondering if anybody knows about an R package to do usual annotations of regions (GC content, mappability, etc), in one package instead of bedtools, and to explore the influence of these biases. I realize the first step can be done with bedtools, and possibly analyzing them in a linear model with RNA seq counts to test their influences (?), but I was just wondering if there was an R option since all analyses are in R data files.

Thanks!

Answer 1

[h.mon]

NOISeq and alpine have severa bias-detection plots / functions.

Answer 2

[jared.andrews07]

Both sva and RUVseq provide methods not only to find hidden batch effects and biases, but also to remove them.