User: Papyrus

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Papyrus210
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Posts by Papyrus

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Answer: A: How can I filter RNA-seq reads to remove reads where more than 50% of the read i
... Assuming you wanted to say " consist of more than 50% low quality ***bases***", I would recommend [fastp][1], it is quite easy to use and has quality filtering options for % of bases within a read not meeting a quality threshold (`--unqualified_percent_limit`, `--qualified_quality_phred` should be w ...
written 14 days ago by Papyrus210
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Answer: C: How to check if there is an association between clustering output (groups) and p
... If I understand correctly, you have clustered your samples into 2 clusters, and want to know if some categorical variables (such as gender) are more represented in one cluster or another? Why don't classify your samples into the 2 clusters and do Chi-squared tests of over-representation of those var ...
written 15 days ago by Papyrus210
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Answer: A: What to choose as background genes in GO enrichment analysis
... I would use all of the genes that were *analyzed* in your experiment: these are those on which you performed the differential expression analyses (you maybe previously filtered them to remove low-expression genes, etc.), because (under assumption of independence) those are the ones which had a chanc ...
written 15 days ago by Papyrus210
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Comment: C: Too many enriched GO terms using Goseq
... Keep in mind that your log2FC values will be positive and negative (for up-regulation and down-regulation, depending on how you specified the contrast). So filter for *absolute* values of log2FC (>1 will be 2x increase (2 FC) and <-1 will be 2x decrease (0.5 FC)). On a side note, if you have ...
written 15 days ago by Papyrus210
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Comment: C: Too many enriched GO terms using Goseq
... It is indeed probably due to your list of DEGs being large. You may also observe that the top of your enrichment list is populated by big GO terms which cover lots of genes (hundreds), because those usually have more power to be detected as enriched due to their big *n*. One thing you could do is t ...
written 15 days ago by Papyrus210
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Comment: C: Whole-genome human-mouse syntenic block tracks/database
... Thanks a lot! I will use this ...
written 16 days ago by Papyrus210
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Whole-genome human-mouse syntenic block tracks/database
... Dear all, I'm trying to find whole-genome tracks of syntenic blocks between human and mouse (hg38-mm10). I've seen several web applications and such, but most are focused on specific regions or genes. Do you know a repository where I can find and download the tracks. I'm sure I must have missed it. ...
genome mouse conservation homology synteny written 16 days ago by Papyrus210
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Comment: C: How to create a GSEA enrichment plot for the phenotypes in R?
... Try this [answer][1] for plotting GSEA output in R This [answer][2] mentions limma's `barcodeplot`. With limma you may perform all the analysis in R, including the plot. (Take note that limma's `camera`gene set analysis is similar, but not equivalent to GSEA) [1]: https://www.biostars.org/p/206 ...
written 17 days ago by Papyrus210
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Comment: C: Pathways analysis taking into account the number of times a gene is present amon
... OK, now I understood your goal. I'm not sure that this is addressed in general in the different types of pathway enrichment analyses: there are gene enrichment approaches where you can input a list of *ranked* genes, and this usually is a fold-change, p-value... For example [GOrilla][1] is a common ...
written 22 days ago by Papyrus210
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Comment: C: Pathways analysis taking into account the number of times a gene is present amon
... No, you do not need expression data. The required input is only a list of genes and background of analyzed genes. And then the parameter for which each gene may be biased. The package then performs enrichment tests to see if there are pathways overrepresented in your list of genes, while taking into ...
written 22 days ago by Papyrus210

Latest awards to Papyrus

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 15 days ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 26 days ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges

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