User: tpm

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tpm10
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Posts by tpm

<prev • 41 results • page 1 of 5 • next >
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Comment: C: How to extract calculated RSA values from dssp and its corresponding residue?
... Thank you, so this code computes relative ASA directly. I will read the link you provided through. ...
written 7 weeks ago by tpm10
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Comment: C: How to extract calculated RSA values from dssp and its corresponding residue?
... To be honest Fatima, I did check, I genuinely think that I don't know how I can extract RSA and its corresponding residue. The actual code is what I am kindly asking in case someone may have passed through this phase. Maybe its because I am not a good programmer, and it can be quite confusing especi ...
written 7 weeks ago by tpm10
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Comment: C: Biopython module Bio.PDB.DSSP issue with solvent accessible surface area?
... How can one make a dataframe for RSA calculated and its corresponding residue. If there are codes to follow up this question above, I would gladly appreciate it very much as I am still in my infancy with regards to coding. Thank you in advance. ...
written 7 weeks ago by tpm10
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How to extract calculated RSA values from dssp and its corresponding residue?
... Hello. I ran this code below from Bio.PDB import * parser = PDBParser() io = PDBIO() structure = parser.get_structure('3F9R', '3F9R.pdb') model = structure[0] dssp = DSSP(model, '3F9R.pdb') residues = list(dssp) residues How do I sele ...
pdb commandline rsa biopython dssp written 7 weeks ago by tpm10
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Comment: C: Input file for CompareCluster in ClusterProfiler
... Great to know that it helped :) ...
written 5 months ago by tpm10
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Answer: C: Input file for CompareCluster in ClusterProfiler
... Hi. Maybe this will in someway help you, I figured to explain from my codes and the idea will weave together at the end. If it will help you feel free to use it. In the example shown from this code, your A, was my excel sheet with ENTREZID and its corresponding logFC [(fold change)] My initial inpu ...
written 5 months ago by tpm10
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Comment: C: How to run protein-protein interaction on R using STRING database
... Its better to check on the website on installations: anyhow if you run this code it will work, if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("STRINGdb") ...
written 5 months ago by tpm10
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Answer: C: compareCluster error: On clusterProfiler DEGs enrichments analysis
... I realized the mistake, which was here 'EC17WT' as I have identical names. I had to change one of them: So not like this $EC17WT [1] "947315" "944895" "947758" "947761" "946796" "948517" $EC17WT [1] "947315" "944895" "947758" "947761" "946796" "948517" but like this: ...
written 7 months ago by tpm10
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compareCluster error: On clusterProfiler DEGs enrichments analysis
... I am working on Clusterprofiler. I am comparing 4 gene sets. I encountered an error, and I am trying to figure out what could be the problem when I run the compareCluster function. I do not know how I can solve this issue. > lapply(LISTcutoff5, head) $EC11WT [1] "947315" "944895" "94 ...
R bioconductor degs clusterprofiler written 7 months ago by tpm10
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Comment: C: How to pull logFC values for a select ENTREZID from a gene-list on R?
... Million thank you. I honestly did not know I could use StackOverflow. I am still a newbie on R :)). Thank you for the clarity. ...
written 7 months ago by tpm10

Latest awards to tpm

Scholar 7 months ago, created an answer that has been accepted. For C: compareCluster error: On clusterProfiler DEGs enrichments analysis

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