User: Radek

gravatar for Radek
Radek50
Reputation:
50
Status:
New User
Location:
Belgium
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 6 months ago
Email:
v*************@gmail.com

Posts by Radek

<prev • 33 results • page 1 of 4 • next >
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Comment: C: scran/scater Normalized matrix
... Thank you !      ...
written 3 months ago by Radek50
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scran/scater Normalized matrix
... Hi! I have a SingleCellExperiment Object. I used the following code to normalise my data: sce <- scran::computeSpikeFactors(sce, general.use = FALSE) scater::normalise(sce) I would like to retrieve the normalised matrix of count afterwards but could not find a proper way to do it. Can someone ...
scran normalized counts scater written 3 months ago by Radek50 • updated 3 months ago by Aaron Lun23k
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karyoploteR: custom genome axis $latest.plot
... Hi!  I would like to dynamically modify the axis from custom genomes plotted with karyoploteR.  Example: library(karyoploteR) custom.genome <- toGRanges(data.frame(chr="chr1", start=1, end=10e7) kp <- plotKaryotype(genome = custom.genome) regions <- GRanges(seqnames=rep( ...
karyoploter written 21 months ago by Radek50
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Circos Tile colors
... Hi! I would like to draw a circos plot representing the aneuploïdy of my samples. My goal is to plot each sample as a different radius of my circle with the color of the tiles representing the aneuploidy (2N, 4N, etc) I started to do some tests using OmicCircos but so far could not find a way to d ...
omiccircos rcircos written 2.0 years ago by Radek50 • updated 24 months ago by bernatgel90
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Comment: C: cn.mops: NA in the output of referencecn.mops
... Hi! As advised I upgraded bioconductor/cn.mops to the lastest version. This seem to have solved the issue.  Thanks for your quick answer.    ...
written 2.4 years ago by Radek50
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cn.mops: NA in the output of referencecn.mops
... Hello! I am currently using cn.mops on several control/tumor samples (WGS).  I used the pipeline for bulk comparison as described by the author: bam <- list.files(path, pattern=".bam$") bamDataRanges <- getReadCountsFromBAM(bam, mode="paired", parallel=2) cn1 <- cn.mops(bamDataRanges) ...
cn.mops referencecn.mops written 2.4 years ago by Radek50 • updated 2.4 years ago by Günter Klambauer540
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Comment: C: Shortread convert S4 vector qualityScore to vector
... Thanks!  Exactly what I was looking for.  ...
written 2.7 years ago by Radek50
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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 2.7 years ago by Radek50 • updated 2.7 years ago by Martin Morgan ♦♦ 23k
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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 3.0 years ago by Radek50
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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 3.0 years ago by Radek50

Latest awards to Radek

Popular Question 3 months ago, created a question with more than 1,000 views. For Limma/DESeq2: Statistic and readcount of biological replicates
Popular Question 23 months ago, created a question with more than 1,000 views. For Limma/DESeq2: Statistic and readcount of biological replicates
Popular Question 23 months ago, created a question with more than 1,000 views. For Affymetrix miRNA 4.0 Normalization and Analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For Differential expression analysis: Continuous variables
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Differential expression analysis: Continuous variables
Commentator 3.0 years 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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