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@qgroom I was reading the section on dwc:occurrenceStatus in the https://doi.org/10.3897/biss.3.38084 paper and it noted "We propose adding notes to the documentation of dwc:occurenceStatus, to point …
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I'm executing `hyperR` with a custom geneset and `"kstest"` weighted by the effect size of a differential expression test. I've noticed, however, that the results I get in `hyp_obj$data` and the dots …
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Asked from a colleague claiming it was better to use "correct" values (ie, given by the RNASeq platform) for fragment length distribution, I tried to use this option. However, I did not understood a f…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/retogerber/censcyt
Confirm the following by editi…
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Hi there, I've ran Differential abundance analysis on my data and have managed to pull out things like top table etc however when I try and run the plotDiffHeatmap it turns up the following error.
…
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Hello,
First of all I really enjoyed reading your paper. It was an excellent analysis that gave me a lot of insight into the various tools. I've been doing a similar analysis so I was interested in…
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Could you specify which edgeR testing method is being used in the `test_differential_abundance` help, is it the likelihood ratio test (LRT) or the quasi-likelihood F-test (QLF)?
e.g. from the edgeR…
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**Submitting author:** @jonschwenk (Jon Schwenk)
**Repository:** https://github.com/jonschwenk/RivGraph
**Version:** v0.4
**Editor:** @kbarnhart
**Reviewer:** @eriknes, @leotrs
**Archive:** 10.5281/ze…
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Hi,
First of all, great plug-in!!!! I think Qurro is a really powerful tool and I have used it successfully so far. However, I wanted to know if there is a way to know the actual value ratios i.e.…
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Currently the method seems fixed to "TMM" in edgeR::calcNormFactors() in test_differential_abundance(). Allowing this to be changed like in scale_abundance() would be nice.