User: etycksen

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etycksen0
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Posts by etycksen

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Answer: A: question on visANT after WGCNA
... I like to filter the visAnt module by edge weight in a similar way you do by simply increasing the stringency until all edges disappear.  Once they all disappear, I then step the filter down one step and then create a node from the sub-network.  I then change the layout to the spoke layout so that t ...
written 2.3 years ago by etycksen0
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Answer: A: RNAseq_Rsubread_transcript variants detection
... The Subread featureCounts functions works great for enumerating unique or multi-mapped reads to genes, but is not the best tool for estimating counts for splice variants due to the added complexity of reads aligning across and between splice junctions for splice variants that contain the same exons. ...
written 2.3 years ago by etycksen0
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Answer: A: How to create "trait data" file for WGCNA
... I assume your interested in finding clusters of genes changing over time in response to two different treatments relative to baseline.  If that is the case, turn your data frame into a model matrix using just the days column, like so: traits <- model.matrix(~day, data = traits.df) ...
written 2.4 years ago by etycksen0

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