User: Qroid

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Qroid40
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2 years, 2 months ago
Joined:
4 years, 7 months ago
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r******************@gmail.com

Posts by Qroid

<prev • 26 results • page 1 of 3 • next >
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Protein inference tool: R package that accepts .mzid files?
... I have MS/MS data that I searched with MS-GF+. Unfortunately, MS-GF+ doesn't do protein inference, so I have a list of peptides in .mzid format. Our workflow is in R. Putting all that together - does there exist an R package which will perform protein inference (i.e. give protein IDs) and accepts . ...
protein protein inference written 2.6 years ago by Qroid40
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ID mapping in Matlab?
... I use Matlab for analysis and I'd like a better, programmatic method of ID mapping, usually from some database ID to a uniprot ID. Right now I'm doing it in a pretty clunky way: upload the database IDs to the uniprot mapping service (http://www.uniprot.org/uploadlists/), download a mapping file, and ...
id matlab mapping written 2.9 years ago by Qroid40
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Comment: C: Protein complex databases - how many are out there?
... Thanks. Do you have a link to the BioGRID complexes? Again I only see pairwise interactions. ...
written 3.5 years ago by Qroid40
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Comment: C: Protein complex databases - how many are out there?
... Is there an easy way to get *complexes* from STRING? My understanding is it's just a list of pairwise interaction. ...
written 3.5 years ago by Qroid40
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Protein complex databases - how many are out there?
... The question is pretty straightforward: what are the published protein complex databases? We typically use CORUM but we're being encouraged to use other databases too, since CORUM is biased to very abundant complexes. A quick Google search shows a few more: - CORUM (http://mips.helmholtz-muenchen.d ...
protein complex protein interaction database written 3.5 years ago by Qroid40 • updated 3.5 years ago by Jean-Karim Heriche23k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Huh, that's very interesting, thank you. Have you used it? Would you recommend it? ...
written 3.6 years ago by Qroid40
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Can you give more detail about translating from Matlab to R being easy? Do you mean that the two languages are similar, or is there an automated tool, or ...? ...
written 3.6 years ago by Qroid40
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Great, thanks! This sounds like a promising option. ...
written 3.6 years ago by Qroid40
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Thanks. I believe Matlab is not standard in proteomics. One option is making a standalone executable (e.g. using Matlab deploytool) meaning no Matlab license is required to run our software, although I'm not sure whether people are any more likely to use it (it's still not R/python). ...
written 3.6 years ago by Qroid40
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... What about if we converted our code to standalone executable? This would get around the expense issue (no Matlab license is needed to run the executable) although not the "uncommon tool" issue. ...
written 3.6 years ago by Qroid40

Latest awards to Qroid

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Batch convert gene numbers (ordered locus names) to protein IDs
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Batch convert gene numbers (ordered locus names) to protein IDs
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Opposite of enrichment analysis

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