Moderator: Bastien Hervé

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Bastien Hervé4.8k
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Karolinska Institutet, Sweden
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Posts by Bastien Hervé

<prev • 814 results • page 1 of 82 • next >
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Answer: A: Problems awking columns from map file
... The error is clear : awk: cmd. line:1: {print $1" "$2" "$3" "$4"} awk: cmd. line:1: ^ unterminated string The `"` after `$4` should be remove Tabulation is a better delimiter than white spaces awk -F '\t' '{print $1"\t"$2"\t"$3"\t"$4}' myfile.map > myfile_f ...
written 3 days ago by Bastien Hervé4.8k
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Answer: A: Consistency of Seurat SCTransform across computers/environments
... After one week on this matter I think it is time to know when to stop digging. Here is where I went so far : https://gist.github.com/Baboon61/4a8dc2e2e433432615a5ba8bae06f249 ---------- https://gist.github.com/Baboon61/69afb6e94c41af05d81b16c85e793dab You can notice that both objects before `SCT ...
written 4 days ago by Bastien Hervé4.8k
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Comment: C: What next after gene list?
... Hello, you can highligth the top ones ...
written 5 days ago by Bastien Hervé4.8k
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Comment: C: Consistency of Seurat SCTransform across computers/environments
... apply10SCTransform.HOME = list() apply10SCTransform.HOME <- mclapply(1:10, function(i) { SCTransform(SCRNARR.HOME, seed.use=1447854, variable.features.n = 2000, vars.to.regress = "percent.mt", verbose = FALSE) }) for (n in 1:9){ print(setdiff(rownames(apply10SCTransform. ...
written 10 days ago by Bastien Hervé4.8k
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Comment: C: Consistency of Seurat SCTransform across computers/environments
... Yeah the objects are the same size every time at the lab and every time the same size at home but objects size are different from the lab compare to the ones I get from home. mclapply(1:10, function(i) { object.size(SCTransform(SCRNARR.LAB, seed.use=1447854, variable.features.n = 2000, va ...
written 11 days ago by Bastien Hervé4.8k
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Comment: C: Consistency of Seurat SCTransform across computers/environments
... Thank you, really interesting thinking ! I dug a bit more into SCTransform and seems like the HVGs are not always the same, see below. Warnings are the same in both cases, the same line is repeated except for warning 31 : #Warnings 29: In theta.ml(y = y, mu = fit$fitted) : iteration limit ...
written 11 days ago by Bastien Hervé4.8k
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Consistency of Seurat SCTransform across computers/environments
... Due to Covid19 situation I am working part time at the lab and at home. At the lab I am working under an HP workstation linux environment and at home on MSI with windows 10 and Rstudio. As input to the SCTransform function I use the same RDS object, same parameters, same R version, same Seurat vers ...
seurat written 12 days ago by Bastien Hervé4.8k
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Comment: C: How can the letters become bigger?
... You have a `label.size` option in the `DimPlot` function. Type `DimPlot R` on google to have the documentation of every R function. Please show some more effort of trying in your future questions. https://www.rdocumentation.org/packages/Seurat/versions/2.3.2/topics/DimPlot ...
written 27 days ago by Bastien Hervé4.8k
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Comment: C: Extract specific regions from list of ncbi nucleotide sequences
... Hi, I think you can do that with [Entrez][1] [1]: https://cran.r-project.org/web/packages/rentrez/vignettes/rentrez_tutorial.html ...
written 28 days ago by Bastien Hervé4.8k
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Comment: C: RNASeq, gtf file
... You can do that in Bash or Python for example. Here are the steps : - Select "transcript" lines - Split by ";" - Look for element starting with "FPKM" - Once found, compare FPKM value to 2. - Keep the line if higher than 2 ...
written 4 weeks ago by Bastien Hervé4.8k

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Scholar 3 days ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Popular Question 9 days ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Great Question 25 days ago, created a question with more than 5,000 views. For Expression using greek letters in R
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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
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Popular Question 3 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
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Popular Question 7 months ago, created a question with more than 1,000 views. For ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue
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