User: arsilan324

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arsilan32460
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Posts by arsilan324

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Is there any quick way to annotate KO terms using a script or tool?
... Hi all, I have a list of KO IDs, and their frequency which I want to annotate. Can you please help me suggesting how can I do so. I have started this manually but it is taking time. But I would appreciate any computational method doing this. KO-Term KO-freq Annotation K13457 49 RPM1, RPS3; ...
ko annotation kegg written 6 days ago by arsilan32460 • updated 6 days ago by Pierre Lindenbaum110k
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... Awesome! It worked perfectly. Many thanks!!! ...
written 17 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... It worked! Thanks! But now another question. It has arranged all the values in ascending order but the genus name is still at the end (common for all). I doubt if it is right. Each column should have its own unique Genus arrangement (if not at all, but at some levels). Do you understand my point? ...
written 18 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... What i get is this > str(sdf1) 'data.frame': 2408 obs. of 74 variables: $ R3.Rhizo.1: int 0 0 0 0 0 0 0 0 0 0 ... $ R3.Rhizo.2: int 0 0 0 0 0 0 0 0 0 0 ... $ R3.Rhizo.3: int 0 0 0 0 0 0 0 0 0 0 ... $ R3.Rhizo.4: int 0 0 0 0 0 0 0 0 0 0 ... $ Genus : int ...
written 18 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... One more question, can I select only top 10 using this command? Or it will sort all. It is taking longer. Running since half an hour and not finished yet... ...
written 18 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... It worked. I worked with txt file but i was using csv initially. Thanks ...
written 18 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... This command is not producing any file! Is it suppose to generate a file? I cannot see any error as well. I am using terminal. head -n 1 seq.csv | tr "\t" "\n" | grep -v Genus | awk '{print NR;}' | while read C; do awk -F '\t' -v C=$C '{printf("%s%s\t%s\n",(NR==1?"#":""),$C,$NF);}' seq.csv > ...
written 18 days ago by arsilan32460
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Comment: C: How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... Not able to understand what the output is? It converts the last column "Genus" into numbers. But I need separately for each each column. ...
written 18 days ago by arsilan32460
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How to re-order (sort) to get top values for each column in excel sheet of OTUs?
... Hi all, I have OTU list with 73 samples (columns) and now I want to extract top 10 for each column including the respective annotation (genus level) provided at the end. This data shows a few only but actually i have hundreds of rows. The data looks like this (subset). Can you please help how to do ...
excel sorting written 18 days ago by arsilan32460 • updated 18 days ago by shenwei3564.0k
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Comment: C: Phyloseq R error: Error in if (xi > xj) 1L else -1L : missing value where TRUE/F
... A subset looks like this SR2_S84 SR3_S85 SR4_S89 SR5_S90 SR6_S91 0 0 0 0 0 0 0.000666183 0 0 0 0 0 0 0 0 0.007258343 0.005995643 0.001528514 0.002698655 0.002695369 When I use the actual numbers, it works; but when i use the percent data (re-standardized), it gives error. Tha ...
written 18 days ago by arsilan32460

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