User: petyuk

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petyuk70
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Posts by petyuk

<prev • 15 results • page 1 of 2 • next >
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Answer: A: MSGF+ is it possible to specify more than one enzyme for digestion in R?
... https://msgfplus.github.io/msgfplus/MSGFPlus.html No, this is not possible. Here is a workaround. Set specificity to "0: Unspecific cleavage" or whatever the right way setting this parameter would be in this package. Then deal with cleavage specificity later. ...
written 4 months ago by petyuk70
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motif enrichment analysis for protein sequences
... Are there any packages for motif enrichment analysis for protein sequences?  I see quite a few for nucleic acid, but surprisingly can't find one for amino acid sequences.   ...
proteiomics written 20 months ago by petyuk70 • updated 20 months ago by Julie Zhu4.1k
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mapping protein PTM data
... Do we have tools to map and visualize PTM data onto protein sequence along with some protein features like structure or functional domains? Perhaps Pbase or Pviz are the way to go, and I'll explore that, but any other tips would be helpful. The image below is an example of what I want to achieve. ...
proteomics written 24 months ago by petyuk70
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Job: junior level position in proteomics/data science
... Basically we are looking for an R hacker to streamline the analysis of proteomics (and sometimes genomics) data. Your actual degree doesn't matter as much as your skills. There are separate job postings on the PNNL's website for applicants with BS, MS and PhD degrees. PNNL is located in the Tri-Citi ...
proteomics job docker git machine learning written 2.1 years ago by petyuk70 • updated 22 months ago by karimse070
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Comment: C: BiocParallel not proceeding
...   If I intercept the execution and rename the host from "WE25743" (the name of my machine) to "localhost", then .bpmakeForkCluster proceeds just fine. Hope that helps.   debugging in: BiocParallel:::.bpmakeForkCluster(8, 10, NA_integer_) debug: { nnodes <- as.integer(nnodes) if (is.na ...
written 3.1 years ago by petyuk70
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Comment: C: BiocParallel not proceeding
... Not sure if this is relevant but this is what I get (regardless of the port). Although may be this is what is supposed to be since there is no process communicating to the 11709 port.  Anyway, BiocParallel:::.bpmakeForkCluster is not cooperating with me today. > port <- 11000L + sample(1000L ...
written 3.1 years ago by petyuk70
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Comment: C: BiocParallel not proceeding
... What is odd it starts with MulticoreParam(), that is FORK type, but later switches to SOCK type.  I thought SOCK is for Windows, but not POSIX systems. ...
written 3.1 years ago by petyuk70
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Comment: C: BiocParallel not proceeding
... Within bpstart the issue is at bpbackend(x) <- .bpmakeForkCluster(nnodes, bptimeout(x), getOption("ports", NA_integer_)) ...
written 3.1 years ago by petyuk70
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Comment: C: BiocParallel not proceeding
... It hits a snag at this line in bplapply BPPARAM <- bpstart(BPPARAM, length(X)) ...
written 3.1 years ago by petyuk70
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Comment: C: BiocParallel not proceeding
... upgrading to BiocParallel_1.7.9 didn't help works fine on windows machine though   ...
written 3.1 years ago by petyuk70

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Student 4.8 years ago, asked a question with at least 3 up-votes. For package specifically dedicated to a manuscript

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