User: petyuk

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petyuk60
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5 days, 1 hour ago
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2 years, 10 months ago
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Posts by petyuk

<prev • 13 results • page 1 of 2 • next >
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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 7 days ago by petyuk60
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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-Cit ...
proteomics job docker git machine learning written 6 weeks ago by petyuk60
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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 13 months ago by petyuk60
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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 13 months ago by petyuk60
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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 13 months ago by petyuk60
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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 13 months ago by petyuk60
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Comment: C: BiocParallel not proceeding
... It hits a snag at this line in bplapply BPPARAM <- bpstart(BPPARAM, length(X)) ...
written 13 months ago by petyuk60
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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 13 months ago by petyuk60
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BiocParallel not proceeding
... After refreshing my R installation and the packages, this simple example of BiocParallel::bplapply doesn't work properly.  It looks like it starts, but never finishes. Thanks for taking a look into it! Vlad   > library(BiocParallel) > fun <- function(v) { + message("working") ## 10 ...
software error written 13 months ago by petyuk60 • updated 12 months ago by Martin Morgan ♦♦ 20k
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Reactome's bug of feature?
... Not sure if this is Reactome's bug or a feature.  A human gene matches to both human and mouse pathways. library(reactome.db) library(AnnotationDbi) pwthws <- as.list(reactomeEXTID2PATHID['55697'])[[1]] mapIds(reactome.db, pwthws,"PATHNAME","PATHID") ...
reactome.db written 2.3 years ago by petyuk60 • updated 2.3 years ago by willem.ligtenberg150

Latest awards to petyuk

Student 2.8 years ago, asked a question with at least 3 up-votes. For package specifically dedicated to a manuscript

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