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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.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

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swh:1:cnt:a711dc6d83969dfe6d8ce63a8f4ec32f19b8ad53
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

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Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
#' Create ExpressionSet.
#'
#' \code{createES} function produces an ExpressionSet object from given data,
#'     and exports it to global scope.
#'
#' @param data Gene expression matrix.
#'
#' @param pData Matrix with phenotypical data.
#'
#' @param varLabels Names of phenoData columns.
#'
#' @param fData Matrix with feature data.
#'
#' @param fvarLabels Names of featureData columns.
#'
#' @return produced ExpressionSet object
#'
#' @import Biobase
#'
#' @examples
#' \dontrun{
#' data <- matrix(1:15, 5, 3)
#' pData <- c("A", "B", "C")
#' varLabels <- "cat"
#' fData <- c("p", "r", "s", "t", "u")
#' fvarLabels <- "id"
#' createES(data, pData, varLabels, fData, fvarLabels)
#' }
#'
createES <- function(data, pData, varLabels, fData, fvarLabels) {
    phenoData <- AnnotatedDataFrame(data.frame(pData))
    varLabels(phenoData) <- varLabels

    featureData <- AnnotatedDataFrame(data.frame(fData))
    varLabels(featureData) <- fvarLabels

    es <- ExpressionSet(assayData = data,
                        phenoData = phenoData,
                        featureData = featureData)
    assign("es", es, envir = parent.frame())
    es
}

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

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