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

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!

r rna-seq annotation
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updated by h.mon h.mon • written by User 7754 User 7754

2 answers

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

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written by h.mon h.mon

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

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written by jared.andrews07 jared.andrews07

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