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 4 months ago by jim.paredes0 • updated 4 months ago by Eric T.2.5k
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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 11 months ago by jim.paredes0 • updated 11 months ago by RamRS22k
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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 11 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 11 months ago by jim.paredes0 • updated 11 months ago by genomax68k
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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 11 months ago by jim.paredes0 • updated 11 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 11 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 2.1 years ago by jim.paredes0

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