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Comment: CAZy database has multiple family sequence...
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
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Recent Replies
Comment: How to corrected test statistics based on the LDSC intercept?
by
Isaac
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Thank you very much!
Comment: Transcription Start Site
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Ming Tommy Tang
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you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
Comment: scRNAseq normalization
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Ming Tommy Tang
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To be honest, I really do not use SCT, and use log normalization all the time...
Comment: Subsetting Seurat object based on list of cell barcodes
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Ming Tommy Tang
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index<- rownames(seurat.obj_combined) %in% all_good_cells_rhemac10$V1 seurat.obj_combined[index, ] should do the trick
Comment: Average expression of a sample in single-cell data
by
dsull
★ 5.6k
Well, if you're only sequencing the very end (the 3' end) of transcripts, how are you going to detect any of the splice junctions that appe…
Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
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swbarnes2
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> Seems like pooling all should be statistically more robust. Yup. So put everything into the same DESeq2 object. See: https://…
Answer: Expert Guidance Required for De Novo Transcriptome Analysis
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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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aUser
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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
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
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
★ 6.9k
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
▴ 390
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…
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