Showing : module-trait relationship • reset
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WGCNA: correlations module-traits, and module membership-gene significance
WGCNA co-expression analysis gene significance module membership module-trait relationship
updated 2.5 years ago by ▴ 10 • written 5.2 years ago by ▴ 40
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Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth I am exploring workflows for differential transcript expression analysis and have been using the nfcore rnasplice pipeline, w…
Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…
Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k
Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…
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Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Comment: ANOVA like approach of edgeR
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