## User: Bioinformatics

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30
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New User
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2 months, 4 weeks ago
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#### Posts by Bioinformatics

<prev • 65 results • page 1 of 7 • next >
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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 3 months ago by Bioinformatics30 • updated 12 weeks ago by Ou, Jianhong1.1k
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... @Aaron Lun Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 4 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 4 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 4 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 4 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 4 months ago by Bioinformatics30 • updated 4 months ago by Gordon Smyth37k
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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 6 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 6 months ago by Bioinformatics30
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... @James W. MacDonald   I just made the parsing smaller in order to show I have tried a lot but I cannot figure out what the problem is. For example  hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id', +                                    'ensembl_peptide_id','ensembl_e ...
written 6 months ago by Bioinformatics30
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... Basically I want to extract all attributes for several genes ,  when I use the following as example, I get an error , would anyone know why? hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','ensembl_peptide_id','ensembl_exon_id', +                                     ...
written 6 months ago by Bioinformatics30 • updated 6 months ago by James W. MacDonald50k

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Popular Question 2.0 years ago, created a question with more than 1,000 views. For unable to update packages: foreign, Matrix

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