User: Oleg Moskvin

gravatar for Oleg Moskvin
Oleg Moskvin60
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United States
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4 years, 6 months ago
Joined:
8 years, 8 months ago
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m******@wisc.edu

Posts by Oleg Moskvin

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Comment: A: goseq: recent update seems to restrict the range of applications
... P.S. I happened to still have an older Bioconductor version on one workstation, and exactly the same pipeline runs without any issues there (goseq_1.16.2).   ...
written 4.5 years ago by Oleg Moskvin60
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goseq: recent update seems to restrict the range of applications
... Hi Matt and Nadia, For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my custom gene sets this way: goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repc ...
goseq written 4.5 years ago by Oleg Moskvin60 • updated 4.4 years ago by Nadia Davidson280
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pathview puzzle
... Hi Weijun, This works perfectly as expected! Thank you for the fast update. This option is indeed destined to be very useful for many researchers. Best, Oleg On 08/30/13, Luo Weijun wrote: > The updated pathview (version 1.1.5) is now available through BioC devel version: > http://biocond ...
process pathview written 5.8 years ago by Oleg Moskvin60 • updated 5.8 years ago by Luo Weijun1.4k
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Answer: A: pathview puzzle
... Hi Weijun, Thank you for the response. The problem seems to be deeper than that and is connected to special handling of a particular species - E.coli - by KEGG. I looked into the pathview() code and here is what I see: 1) gene.data is remapped internally via mol.sum() to have ENTREZ IDs; 2) rema ...
written 5.8 years ago by Oleg Moskvin60
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pathview puzzle
... Colleagues, I'd like to use pathview with E.coli data. While the Homo sapience example from the manual works just fine: pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = demo.paths$sel.paths[i], species="hsa", out.sufix="gse1683", kegg.native=TRUE) using an analogous run with E.col ...
pathways pathview written 5.8 years ago by Oleg Moskvin60
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IRanges, GenomicRanges, GenomicFeatures?
... Hello list members, For a RNA-seq analysis, what would you suggest to use to convert raw- sequence-based read coverage to annotated ORF-based coverage, if the genome of interest is NOT supported in neither UCSC nor ENSEMBL, which means that creation of a TranscriptDB object in a straightforward way ...
coverage annotation transcriptdb convert genomicfeatures written 8.6 years ago by Oleg Moskvin60 • updated 8.6 years ago by Steve Lianoglou12k
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Answer: A: Illumina DGE => sRNA detection pipeline
... Hi Sean, Thank you for the hints. I see what you mean. Since ChiP-seq workflow is inevitable here and I don't have experience with that, I should rephrase and narrow down my question to "which Bioconductor/R tools are the best at the moment to genome coverage visualization and differential express ...
written 8.7 years ago by Oleg Moskvin60
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Illumina DGE => sRNA detection pipeline
... Hello list members, I usually work in R environment for most of my projects. I am interested in using R/Bioconductor to detect small RNA species in Illumina DGE data. After reviewing available Bioconductor packages, I have an impression that there is no establisted pipeline to do that (is that true ...
written 8.7 years ago by Oleg Moskvin60

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