User: ladypurrsia

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ladypurrsia30
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8 months, 1 week ago
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2 years, 3 months ago
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Posts by ladypurrsia

<prev • 17 results • page 1 of 2 • next >
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Comment: A: Network plot from expression data in R using igraph
... Thank you so much for this tutorial. I have applied it to my data and it works fantastic. I would like to ask about something though. I followed your directions exactly in creating a pearson correlation distance: g <- graph.adjacency( as.matrix(as.dist(cor(t(POS_NSp), method="pearson" ...
written 8 months ago by ladypurrsia30
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Comment: C: Nested Bubble Plots
... Thank you, Kevin. At least you suggested a starting point. I can probably build from here. Yes - first thing I did was read the methods section of the paper - zero mention of that graph. If they had mentioned at least something about it - I would not have posted!! ...
written 8 months ago by ladypurrsia30
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(Closed) Nested Bubble Plots
... Dear community members: I ran into this image from a paper (Vieira et al., 2016: Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata). It's [Figure_3][1] of the paper. ...
taxonomy bubble plots written 8 months ago by ladypurrsia30
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Nested Bubble Plots
... Dear community members: I ran into this image from a paper (Vieira et al., 2016: Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata); it's Figure 3 and I put it in thi ...
taxonomy bubble plots written 8 months ago by ladypurrsia30 • updated 8 months ago by h.mon26k
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Pathview parsing error
... Dear Biostars community: I have recently downloaded the package pathview from Bioconductor. My dataset is a matrix that looks like this: head SP.KEGG log2FoldChange K00005 -1.5503608 K00045 -0.7369513 K00150 -1.4072273 K00214 -1.3487558 K00218 -1.806 ...
R pathview parsing written 20 months ago by ladypurrsia30 • updated 14 days ago by SMK1.8k
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Comment: C: How do I go from UniProt ID to retrieving the gene name?
... Here is Uniprot's link that explains about programmatic (i.e. terminal) access to the retrieve/mapping tool: [Programmatic access - Mapping database identifiers][1] They have examples on how to write a script in several languages just for this. Also, If you are unfamiliar with how to use the UniPro ...
written 20 months ago by ladypurrsia30
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Comment: C: Using UniProt's Retrieve/ID mapping service programmatically to retrieve Taxonom
... Pierre: My apologies. I have just added the link to that particular question to this question. ...
written 2.1 years ago by ladypurrsia30
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Using UniProt's Retrieve/ID mapping service programmatically to retrieve Taxonomy from ACC_ID
... I have completed a blastx run on my samples and have obtained the following result (example): $head blastx_result.txt NS500162:172:HG5CJBGXX:1:11101:2522 ZWIP2_ARATH 52.500 40 19 0 2 121 25 64 8.26e-07 44.3 I would like to take the ACC_ID number, in this case, ZWIP2_ARATH and find the taxonom ...
taxonomy blastx uniprot written 2.1 years ago by ladypurrsia30 • updated 2.1 years ago by Elisabeth Gasteiger1.6k
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Comment: C: Retrieving Taxonomy from Uniprot/Swissprot ACC_ID From Blastx Results
... Pierre: Thank you so much!!! May I ask - is there a way to give a file of these ACC_IDs? Because I have > 500,000 to look up and I cannot input each one manually. ...
written 2.1 years ago by ladypurrsia30
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Retrieving Taxonomy from Uniprot/Swissprot ACC_ID From Blastx Results
... I have completed a blastx run on my samples and have obtained the following result (example): $head blastx_result.txt NS500162:172:HG5CJBGXX:1:11101:2522 ZWIP2_ARATH 52.500 40 19 0 2 121 25 64 8.26e-07 44.3 I would like to take the ACC_ID number, in this case, ZWIP2_ARATH and find the taxonom ...
taxonomy blastx uniprot written 2.1 years ago by ladypurrsia30

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Popular Question 20 months ago, created a question with more than 1,000 views. For Using UniProt's Retrieve/ID mapping service programmatically

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