Question: R package to annotate and explore effect of biases in RNA Seq
1
gravatar for User 7754
21 months ago by
User 7754240
United Kingdom
User 7754240 wrote:

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!

annotation rna-seq R • 466 views
ADD COMMENTlink modified 21 months ago by h.mon29k • written 21 months ago by User 7754240
2
gravatar for h.mon
21 months ago by
h.mon29k
Brazil
h.mon29k wrote:

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

ADD COMMENTlink written 21 months ago by h.mon29k
0
gravatar for jared.andrews07
21 months ago by
jared.andrews075.5k
St. Louis, MO
jared.andrews075.5k wrote:

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

ADD COMMENTlink written 21 months ago by jared.andrews075.5k
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