User: sandmann.t

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sandmann.t20
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Posts by sandmann.t

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Annotating outdated SNP identifiers
... Dear Bioconductors, I have a long list of dbSNP identifiers (e.g. rs7335199), some of which are outdated and now represented by a new identifier. For example, the following call to ensembl's REST API reveals that variant rs7335199 is now referred to as rs3. curl 'https://rest.ensembl.org/variant ...
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Comment: C: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
... Thanks a lot for sharing your workflow! Just curious: the titles says "Analysis of Lexogen Quantseq Data: Part 1". Is there a "Part 2" anywhere? ...
written 6 months ago by sandmann.t20
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Does GSEABase support organismDb objects?
... Dear Martin, thanks a lot for implementing the awesome GSEABase infrastructure. Especially the conversion between identifiers is something I use a lot. So far, I had been annotating my GeneSet objects by referencing orgDb objects (e.g. org.Mm.eg.db). Once I noticed that there are the OrganismDb wr ...
gseabase written 9 months ago by sandmann.t20
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Answer: A: Help with error: 'pd.u133aaofav2 was not found in the BioConductor repository'.
... As Guido pointed out, the ArrayExpress function from the ArrayExpress package does not automatically use the current Bioconductor annotation package for this array type. As this functionality is provided by the ArrayExpress package (not by gCMAPWeb), I have contacted its maintainer to highlight this ...
written 10 months ago by sandmann.t20
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Answer: A: Mismatched ArrayExpress microarray annotation package
... For anybody else who get's stuck, here is a workaround for the E-GEOD-5258 Connectivity Map dataset, which could also be applied to other datasets as well: library(ArrayExpress) # global variables kAccession <- "E-GEOD-5258" kDataDir <- "~/data_dir" # retrieve the raw data from ArrayExpress ...
written 10 months ago by sandmann.t20
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Mismatched ArrayExpress microarray annotation package
... Dear Bioconductors, I am contacting you because you are listed as the maintainer of the ArrayExpress Bioconductor ArrayExpress package. I tried to use the ArrayExpress function to access a large dataset stored in ArrayExpress: "E-GEOD-5258" library("ArrayExpress") GEOD5258.batch <- ArrayExpres ...
arrayexpress hthgu133a.db written 10 months ago by sandmann.t20
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Comment: C: Sparse matrices in Bioconductor objects for single-cell analyses
... That's great! Thanks a lot for sharing your progress, plans and especially the pointer to the SingleCellExperiment package. I am not surprised that you have even more awesome solutions in the works :-) ...
written 10 months ago by sandmann.t20
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Sparse matrices in Bioconductor objects for single-cell analyses
... Dear Bioconductors,  more and more publications include large single-cell RNA-seq datasets. For example, Keren-Shaul et al made count matrices with 34016 gene x 37248 samples (= cells) available on NCBI GEO. I am interested in using Bioconductor to analyze such data and was happy to find the single ...
workflows scater simplesinglecell written 10 months ago by sandmann.t20 • updated 10 months ago by Aaron Lun19k
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Comment: C: Bioconductor docker images without Rstudio-server?
... Completely agree, it makes total sense to take advantage of the work rocker has already invested in installing RStudio server. Thank you for pointing out that I can include the removal step in my Dockerfile. I hadn't even thought that far, yet. apt-get remove didn't work for me, but  dpkg --remov ...
written 22 months ago by sandmann.t20
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Comment: C: Bioconductor docker images without Rstudio-server?
... Thank you, Dan. I agree that the number of people benefiting from RStudio server is large. I will follow your advice and build my own images. That said, docker makes it pretty easy to add a layer; removing one isn't as convenient. Starting with r-base, adding Bioconductor and - in a final layer - R ...
written 22 months ago by sandmann.t20

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