User: Radek

gravatar for Radek
Radek40
Reputation:
40
Status:
New User
Location:
Belgium
Last seen:
1 month, 4 weeks ago
Joined:
3 years ago
Email:
v*************@gmail.com

Posts by Radek

<prev • 31 results • page 1 of 4 • next >
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karyoploteR: custom genome axis $latest.plot
... Hi!  I would like to dynamically modify the axis from custom genomes plotted with karyoploteR.  Example: library(karyoploteR) custom.genome <- toGRanges(data.frame(chr="chr1", start=1, end=10e7) kp <- plotKaryotype(genome = custom.genome) regions <- GRanges(seqnames=rep( ...
karyoploter written 15 months ago by Radek40
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Circos Tile colors
... Hi! I would like to draw a circos plot representing the aneuploïdy of my samples. My goal is to plot each sample as a different radius of my circle with the color of the tiles representing the aneuploidy (2N, 4N, etc) I started to do some tests using OmicCircos but so far could not find a way to d ...
omiccircos rcircos written 18 months ago by Radek40 • updated 17 months ago by bernatgel90
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Comment: C: cn.mops: NA in the output of referencecn.mops
... Hi! As advised I upgraded bioconductor/cn.mops to the lastest version. This seem to have solved the issue.  Thanks for your quick answer.    ...
written 23 months ago by Radek40
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cn.mops: NA in the output of referencecn.mops
... Hello! I am currently using cn.mops on several control/tumor samples (WGS).  I used the pipeline for bulk comparison as described by the author: bam <- list.files(path, pattern=".bam$") bamDataRanges <- getReadCountsFromBAM(bam, mode="paired", parallel=2) cn1 <- cn.mops(bamDataRanges) ...
cn.mops referencecn.mops written 23 months ago by Radek40 • updated 23 months ago by Günter Klambauer510
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Comment: C: Shortread convert S4 vector qualityScore to vector
... Thanks!  Exactly what I was looking for.  ...
written 2.2 years 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 2.2 years ago by Radek40 • updated 2.2 years ago by Martin Morgan ♦♦ 22k
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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 2.5 years 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 2.5 years 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 2.5 years 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 2.5 years ago by Radek40 • updated 2.5 years ago by Aaron Lun21k

Latest awards to Radek

Popular Question 17 months ago, created a question with more than 1,000 views. For Limma/DESeq2: Statistic and readcount of biological replicates
Popular Question 17 months ago, created a question with more than 1,000 views. For Affymetrix miRNA 4.0 Normalization and Analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For Differential expression analysis: Continuous variables
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Differential expression analysis: Continuous variables
Commentator 2.5 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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