User: antonioggsousa

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antonioggsousa1.5k
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Posts by antonioggsousa

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Answer: A: questions about qiime2 manifest file; error message: semantic type SampleData[Se
... Hi, Ideally you should post questions related with QIIME2 in their forum, since they put their efforts to provide feedback on QIIME2 users under their platform at: https://forum.qiime2.org/ Although I think the problem is your `manifest` file. You shouldn't change the header of the table and you ...
written 19 hours ago by antonioggsousa1.5k
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Understand GTF produced by StringTie
... Hi, I'm collaborating in a project where the transcriptome of *Arabidopsis thaliana* was assembled with [StringTie](https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual). Since the aim of the project is also to look into the long-non-coding RNA transcripts, just a few of them were kept. I ...
assembly rna-seq written 19 hours ago by antonioggsousa1.5k
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... I don't think that you can do that, but I may have be wrong. So, a PCA or PCoA is a multivariate method. So you need to have a set of observations across several (usually a few-to-thousand) variables. In your case I don't see which can be observations or variables. That's why a PCoA is used in bet ...
written 10 days ago by antonioggsousa1.5k
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Comment: C: sortmerna error ref file
... Please, edit your post to make it clear and use the insert code button to highlight the code. As it is it is quite hard to read the code from the text. From the error message it seems that you have a problem with the paths that you're providing. Perhaps giving absolute file/folder paths will make ...
written 10 days ago by antonioggsousa1.5k
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Comment: C: Unable to run pdflatex
... Hi, I never used that package, so I'm not familiar with it. From the error message - `! TeX capacity exceeded, sorry [save size=80000].` - it seems that you cannot run `pdflatex` because you run out of RAM memory or the memory exceed by the program. Therefore, the memory that you've is not enough ...
written 10 days ago by antonioggsousa1.5k
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Or I don't understand what you're trying to do or I'm not familiar with the analysis that you want to do. Can you provide a reference paper that highlights a similar analysis to the one that you want to do, please? From your description and based on my background on microbial ecology, this sounds l ...
written 10 days ago by antonioggsousa1.5k
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Comment: C: Use PCoA plot rather than phylogenetic tree?
... Can you edit your post and make it clear, please. Which data do you have and what do you want to highlight through the PCoA? ...
written 11 days ago by antonioggsousa1.5k
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Answer: A: SparCC repository gone
... Hi, I do not have the SparCC scripts. You may need to contact the authors of the tool. I think there is a fast version of SparCC: https://github.com/shafferm/fast_sparCC There is also an implementation in R within the SpiecEasi R package: https://www.rdocumentation.org/packages/SpiecEasi/versio ...
written 14 days ago by antonioggsousa1.5k
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Answer: A: Appending output to a vector in R
... Hi, You can set the size of the vector and use indexing to index and change the vector. Or you can use the function `append()`, to **append** a value to a vector. In any case you need to iterate over a sequence. n <- 100 ctrl <- c(rep(NA, n)) # a vector with NAs across 100 pos ...
written 4 weeks ago by antonioggsousa1.5k
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Comment: C: problem in generating correlation heatmap with significance level
... Hi, The error is because you do not have the `Method` object. Try to use the R `corrplot` package: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html I think it does what you want and it is fairly well documented. António ...
written 4 weeks ago by antonioggsousa1.5k

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