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Hi!
I'm not very familar with GRN, I got some questions after reading GENIE3 vignette.
1. Is that sample number matters? What's a proper sample number?
2. Is the treat method of sample matters?…
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From my exposure to classic WGCNA and this package so far, it seems like classic WGCNA often assigns most genes to a module and leaves a very small grey module (especially when using filtered genes as…
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Is CarDEC applicable to bulk RNA seq data? I have a relatively large dataset (~1300 samples from 70 experiments) that I’d like to correct for significant batch effects
mdanb updated
3 years ago
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Hi,
I have bulk RNA-seq data with one fixed effect (Condiiton) and 2 random effects (patients and batch Info). I am running dream to perform DE analysis.
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Hello,
This is more of a question than an issue, but I would like to run velocyto on bulk, 100x100 RNA-seq. I have 6 samples currently, all with >30m reads. Is there any particular way you would su…
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I think your proposed experiment is well designed, has an adjustable scope that you can expand on later down the line, and has very clear short- and long-term goals.
I have a minor proposition. Wha…
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Does TElocal work with long read bulk RNA-seq? If so, has anyone done this, and, are there any reccomrecommendations on how to run it?
Thank you,
FR
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I have read in your documentation that
**_The new.prism function removes any genes in the mixture greater than 1% in more than 10% of the mixture samples by default. This threshold is very lenient…
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Hello,
I am trying to use SCnorm to normalize bulk RNA-seq data. I have about 10 studies with differing numbers of samples. I removed any genes that have no counts in any samples. I then used the a…
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Sub-task of #2
- [ ] 1a. BrainSpan DLPFC bulk RNA-seq
- [ ] 1b. LIBD BrainSeq DLPFC data
- [ ] 1c. non-human primate laser microdissection (gene expression microarrays)