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RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
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
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Doomhammer
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Do you have enough clean data to assemble, for each genotypes independently? I think at first we should find the difference in transcripts …
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Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
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Dora
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Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
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Chris
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Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
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sooni
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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
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Chris Dean
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That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
Answer: Beagle Phasing and Imputation
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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
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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…
Answer: Seurat 5 integration
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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…
Answer: scRNAseq normalization
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ATpoint
81k
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
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el24
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Here is a simple pythonic way to use biomart: import pybiomart as pbm dataset = pbm.Dataset(name='hsapiens_gene_ensembl', host="h…
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