User: Radek

gravatar for Radek
Radek40
Reputation:
40
Status:
New User
Location:
Belgium
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 9 months ago
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Posts by Radek

<prev • 30 results • page 1 of 3 • next >
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Circos Tile colors
... Hi! I would like to draw a circos plot representing the aneuploïdy of my samples. My goal is to plot each sample as a different radius of my circle with the color of the tiles representing the aneuploidy (2N, 4N, etc) I started to do some tests using OmicCircos but so far could not find a way to d ...
omiccircos rcircos written 9 weeks ago by Radek40 • updated 9 weeks ago by bernatgel60
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Comment: C: cn.mops: NA in the output of referencecn.mops
... Hi! As advised I upgraded bioconductor/cn.mops to the lastest version. This seem to have solved the issue.  Thanks for your quick answer.    ...
written 7 months ago by Radek40
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cn.mops: NA in the output of referencecn.mops
... Hello! I am currently using cn.mops on several control/tumor samples (WGS).  I used the pipeline for bulk comparison as described by the author: bam <- list.files(path, pattern=".bam$") bamDataRanges <- getReadCountsFromBAM(bam, mode="paired", parallel=2) cn1 <- cn.mops(bamDataRanges) ...
cn.mops referencecn.mops written 7 months ago by Radek40 • updated 7 months ago by Günter Klambauer420
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Comment: C: Shortread convert S4 vector qualityScore to vector
... Thanks!  Exactly what I was looking for.  ...
written 10 months ago by Radek40
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Shortread convert S4 vector qualityScore to vector
... Hello! I having some difficulties to convert a S4 vector to a vector in the shortRead package. I simply would like to trim the sequences contained in a shortReadQ object and their associated quality scores based on a vector (filterTable$start). Such as: # Read the fastq file fq <- readFastq ...
shortread written 10 months ago by Radek40 • updated 10 months ago by Martin Morgan ♦♦ 20k
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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... Hello! Is it possible that you forgot the "=" in  DESeqDataSetFromMatrix(countData = counts,colData = mycols, design = ~ condition) ? ...
written 14 months ago by Radek40
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Comment: C: Pool Single-cells: Analysis
... Unfortunately the cost is not the main reason. Those cells are really tricky to get. I'll see if it will be possible to screen 10 plates per animals to increase the number of harvested cells. But thanks for your answers, your advices are more than welcome.  ...
written 14 months ago by Radek40
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Comment: C: Pool Single-cells: Analysis
... Thanks this is a great summary! I don't want to absolutely use DESeq2/edgeR. It is just the one that I know the best currently. I'll follow your advices and have a deeper look to packages dedicated to single-cells. Based on what you discuss, the number of cells pooled will be a key factor. We had t ...
written 14 months ago by Radek40
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Pool Single-cells: Analysis
... Hello! We are thinking doing RNA-seq on single-cells. Due to some constraints related to the biological model we are planning to pool a small amount of cells together (2 to 10) and perform RNA-seq on this pool. The experimental question behind is a classical transcriptome comparison of groups that ...
limma deseq2 voom single cell written 14 months ago by Radek40 • updated 14 months ago by Aaron Lun15k
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Comment: C: DESEq2 - Why is "my gene" not differentially expressed?
... Even if it can be done, you're maybe skewing a little bit the data.  To me (but I can be wrong, especially because I don't know which gene/system you're studying) you need to consider the two opposite opinions here: It is good practice to check for what is known. So if you don't find something tha ...
written 15 months ago by Radek40

Latest awards to Radek

Popular Question 14 months ago, created a question with more than 1,000 views. For Differential expression analysis: Continuous variables
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Problem making DESeq dataset; Error all variables in design formula must be colu

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