## User: Bioinformatics

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#### Posts by Bioinformatics

<prev • 67 results • page 1 of 7 • next >
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Comment: C: how can I find a pathway
... @mahmoud.s.fahmy finding which pathways those molecules are belonging to ...
written 6 days ago by Bioinformatics30
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... I have a Metabolomics data with a p value, I want to know which ways I can find pathways, as an example please use the following data df<- structure(list(rn = c("1-Methylhistidine", "L-Kynurenine", "N6,N6,N6-Trimethyl-L-lysine", "Putrescine", "Cytidine", "Xanthosine", "N-Alpha-acetyllys ...
written 11 days ago by Bioinformatics30
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... I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino- ...
written 8 months ago by Bioinformatics30 • updated 8 months ago by Ou, Jianhong1.2k
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... @Aaron Lun Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 10 months ago by Bioinformatics30
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... @Gordon Smyth Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 10 months ago by Bioinformatics30
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... @ Aaron Lun I did read that part for sure, I cannot estimate the dispersion because I don't have many housekeeping genes so I set it as 0.4 which I think it is a good number between 0.1 and 0.6. Yes  estimateGLMCommonDisp does not work due to problem you mentioned. I am just wondering if there i ...
written 10 months ago by Bioinformatics30
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... @Gordon Smyth these are normalized expression not count. so it means if people do not use raw count, it won't be trusted? I have read many papers they published in science with FMPK which is normalized count by length of gene analyzed by edger !! (I personally do not like FMPK but just as example. ...
written 10 months ago by Bioinformatics30
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... Hi, I have a representative data like this. the first column is control and second is treated df<- structure(list(col1A = c(1.64, 0.03, 0, 4.202, 2.981, 0.055, 0, 0.002, 0.005, 0, 0.002, 0.649, 2.55, 2.762, 6.402, 0.91, 0.037, 0, 5.757, 3.916, 0.022, 0, 0, 0.003, 0, 0.262, 0.136, ...
written 10 months ago by Bioinformatics30 • updated 10 months ago by Gordon Smyth39k
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... @James W. MacDonald gene ontology means you can find various information from any given gene. Look at http://www.geneontology.org    ...
written 12 months ago by Bioinformatics30
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... @James W. MacDonald basically I am trying to do gene onthology. there are 100 packages but I prefer to retrieve data from UniProt or ensemble.  ...
written 12 months ago by Bioinformatics30

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