User: sHeyne

gravatar for sHeyne
sHeyne30
Reputation:
30
Status:
New User
Location:
Freiburg, Germany
Last seen:
3 months ago
Joined:
2 years, 4 months ago
Email:
s************@gmail.com

Posts by sHeyne

<prev • 4 results • page 1 of 1 • next >
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Comment: C: ERROR when I run Pathview()
... Can you fix this in the pathview package? See my answer! ...
written 4 months ago by sHeyne30
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Answer: A: ERROR when I run Pathview()
... I also run into the same problem. I think the solution is to name the right package/namespace within geneannot.map() from pathview, ie. AnnotationDbi::select(), to be not in conflict with select from dplyr! in my version I changed line 52 in function `geneannot.map()` from res <- try(su ...
written 4 months ago by sHeyne30
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Answer: A: Strange MA-plot using DESeq2
... The red cloud at the bottom looks like a contamination from some other cell/tissue type (in case of eg. mouse or human). In your case, all samples/replicates are from "whole body" beetles? Don't know how this then could happen... In order to see if this effect relates to one or more replicates, you ...
written 11 months ago by sHeyne30
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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... Methods like Salmon seem powerful and they overall do a good job, however recently I stumbled upon the (at least Salmon's) behavior on "multi" vs "uniquely" mapping reads (in featureCounts/htseq-count terms, Salmon uses SMEMs/k-mers). Eventhough there are some parameters to influence salmon like ...
written 2.4 years ago by sHeyne30

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Strange MA-plot using DESeq2

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