User: jirkanov

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jirkanov0
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Posts by jirkanov

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Comment: C: Using DESeq2 for T-cell receptor clonotypes
... Sure, I was just a little bit confused with the formulation "you may want" :-) Many thanks Michael! And by the way, thumbs up for your talks at CSAMA2018, they were fantastic :-) Unfortunately, at that time, I didn't have those data to ask you personally... ...
written 5 weeks ago by jirkanov0
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Comment: C: Using DESeq2 for T-cell receptor clonotypes
... OK. And should I use fitType=“mean”? ...
written 5 weeks ago by jirkanov0
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Comment: C: Using DESeq2 for T-cell receptor clonotypes
... Thanks for quick answer. Here it is: ...
written 5 weeks ago by jirkanov0
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Using DESeq2 for T-cell receptor clonotypes
... Hello, I need to do a differential expression analysis of T-cell receptor (TCR) clonotypes. Simplified, TCRs are special proteins (part of immune system) which can recognize various another proteins. Because of their dynamic recognition abilities, gene encoding TCR has variable regions which are di ...
deseq2 immunology tcr clonotypes written 5 weeks ago by jirkanov0 • updated 5 weeks ago by Michael Love19k
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HTqPCR - unable to create a 'qPCRset' object
... Hello, I am unable to create a 'qPCRset' object from my own data: cp_matrix[1:5, 1:5] VM12B_1_8R VM12B_2_9L VM12B_3_33R VM12B_4_50L VM12B_2_20L Nppa 36.74 25.33 26.80 26.02 25.05 Myh7 25.37 22.17 25.04 22.33 25.01 Atp2 ...
htqpcr expressionset written 8 weeks ago by jirkanov0
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Comment: C: How to add more columns to ReportingTools output?
... Thanks, good solution! I didn't realize publish is internally using topTable which in fact generates a data.frame. I will definitely look at your package, looks handy. I haven't mentioned I need only genes with specific GO IDs (I know I am deleting duplicates in my example; that code line shouldn't ...
written 9 months ago by jirkanov0
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How to add more columns to ReportingTools output?
... Hello, I am doing differential expression analysis from Illumina microarray. Annotation package for microarray (illuminaHumanv3.db) contains a lot of useful information which I want to be included in ReportingTools HTML table (e.g. GO ID). How to include this additional information (columns respect ...
microarray annotation reportingtools differential expression differential analysis written 9 months ago by jirkanov0 • updated 9 months ago by James W. MacDonald47k

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