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Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential expression at pathway level
A: Difference between heatmap using Euclidian distance and Poisson distance
A: Difference between heatmap using Euclidian distance and Poisson distance
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Recent Replies
Comment: Differential express genes in imbalance groups
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Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
sooni
▴ 20
It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
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Gordon Smyth
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I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
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LChart
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Not doable with older versions of beagle. I seem to recall that it used to be recommended to re-code the sex chromosomes of males in the re…
Answer: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
Imbalanced group sizes are no problem. Just analyse the data as it is. No need to throw data away! For a human study with a large number o…
Comment: Trim Galore: Automatic detection of adapters
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Daniel
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Got it, this clears things up. Thank you!
Answer: basal gene expression level
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LChart
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I haven't seen any reliable way to estimate absolute RNA concentrations from sequencing data. Methods have been developed using [housekeepi…
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jared.andrews07
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You are still free to change whichever parameters you want for whichever method you're using. See `?IntegrateLayers` and whichever method y…
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ATpoint
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It's perfectly fine to use log-transformation. The advantages of these more complicated methods usually depend on context and also on the w…
Answer: scRNAseq normalization
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dsull
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No, your log-transform might indeed be ok (or even better) for your analysis of interest. See https://www.nature.com/articles/s41592-023…
Answer: Transcription Start Site
by
el24
▴ 40
Here is a simple pythonic way to use biomart: import pybiomart as pbm dataset = pbm.Dataset(name='hsapiens_gene_ensembl', host="h…
Comment: data background noise
by
marco.barr
▴ 30
Thank you very much for your response. I've been calling it background noise, but perhaps we're saying the same thing. I mean, I really wan…
Comment: Average expression of a sample in single-cell data
by
newuser2024
• 0
Thank you for your reply. Sorry to ask this but could you explain how 3' tag can effect splicing detection, please?
Comment: blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
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SequenceServer
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Ugh that's frustrating. Are you using the same version of Linux and all data files too? BLAST has some dependencies that may have also ch…
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