Bioconductor Cytobank_to

Showing : cytobank_to_gatingset • reset

0

votes

2

replies

1.0k

views

CytoML cytobank_to_gatingset

4.3 years ago km_sch2002 • 0

1 result • Page 1 of 1

Recent ...

Replies

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…

Votes

Comment: ANOVA like approach of edgeR

Awards • All

Popular Question to Marek Gierlinski ▴ 30

Scholar to Gordon Smyth 52k

Popular Question to mohammedtoufiq91 ▴ 10

Popular Question to Hans-Ulrich Klein ▴ 330