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Revision 9f7b6d4e450c337560b4a6df9198aa74c9be01b9 authored by Vladislav Kamenev on 07 August 2018, 09:41:33 UTC, committed by GitHub on 07 August 2018, 09:41:33 UTC
Merge pull request #85 from ctlab/develop
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2 parent s d144ef5 + 39a8be5
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  • shinyGAM.R
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To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
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Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
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Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
shinyGAM.R
#' Constructs data frame with gene annotations and submits it into Shiny GAM web-server
#' @param es Expression set object
#' @return URL for Shiny GAM
#' @importFrom utils write.table
shinyGAMAnalysis <- function(es) {
    de <- fData(es)

    deFile <- tempfile()
    write.table(de, deFile, sep="\t", row.names=FALSE, col.names=TRUE)

    # :ToDo: deal with bad certificates and remove ssl_verifypeer option
    r <- httr::POST(url="https://artyomovlab.wustl.edu/upload",
               body=readBin(deFile, what="raw", n=20e6),
               httr::config(ssl_verifypeer = FALSE))
    httr::stop_for_status(r)
    key <- httr::content(r, as="text", encoding="UTF-8")

    shinyGAMUrl <- sprintf("https://artyomovlab.wustl.edu/shiny/gam/?geneDE_key=%s", key)
    return(jsonlite::toJSON(shinyGAMUrl))
}
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