User: jim.paredes

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Posts by jim.paredes

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CNVkit Heatmap samples clustering
... Hello! Iunderstand that CNVkit plots the heatmap ordering the samples alphabetically or following a provided order; but, I need to make a clustering for the samples. I need to plot them according to a mathematical order to see which samples are similar or different regarding Log2 value. I want to kn ...
cnvkit cnv clustering heatmap written 5 days ago by jim.paredes0
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Comment: C: copy number file format issue
... Ok, well, the original file is .cns, it is a text file, that looks like this (first line plus header): chromosome,start,end,gene,log2 chr1,13402,861395,"LOC102725121,DDX11L1,OR4F5,LOC100133331,LOC100132062,LOC100132287,LOC100133331,LINC00115,SAMD11",-0.28067 We transformed it to a .csv so ...
written 7 months ago by jim.paredes0 • updated 7 months ago by RamRS20k
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Comment: C: copy number file format issue
... The format is not really the problem, I can export it to any other format, but, the genes column looks the same. How can I do it with Python? ...
written 7 months ago by jim.paredes0
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Comment: C: copy number file format issue
... Thanks! I was trying with this mostly: awk -F , -v OFS='\t' 'NR == 1 || $0 > 0 {print $4}' AGM3.call.prueba.cns.csv |less But, it doesn't work well. And also, I need to repeat the Log2 value for each gene in the row (in the comma separated list). Would transpose the columns work for this? ...
written 7 months ago by jim.paredes0 • updated 7 months ago by genomax62k
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copy number file format issue
... Hello, I have a problem with a .csv file from Copy number data. The original looks like this: genes Log2 PIK3CA,TET2 -0.35 MLH2,NRAS 0.54 And, what I need is: genes Log2 PIK3CA -0.35 TET2 -0.35 ...
R copynumber cnv python written 7 months ago by jim.paredes0 • updated 7 months ago by cpad011211k
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(Closed) csv file, columns issue
... **Hello, I have a problem with a .csv file from Copy number data. The original looks like this:** genes Log2 PIK3CA,TET2 -0.35 MLH2,NRAS 0.54 **And, what I need is:** genes Log2 ...
R comma columns cnv python written 7 months ago by jim.paredes0
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Comment: A: Request to BioMart web service failed. Verify if you are still connected to the
... Hi! i had the same error and tried to solve it as you did, but now it gives me this error: Error: XML content does not seem to be XML: I don´t know to fix it. Could you help me please? ...
written 21 months ago by jim.paredes0

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