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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:3fe0b7b59fc79aaac69f3b4432a1af31ee558bb3
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 ...
limmaAnalysisImpl <- function(es, fieldValues) {
    fieldValues <- replace(fieldValues, fieldValues == "", NA)

    es.copy <- es
    es.copy$Comparison <- fieldValues
    fData(es.copy) <- data.frame(row.names = rownames(es.copy))

    es.copy <- es.copy[, !is.na(es.copy$Comparison)]

    # Getting rid of check NOTEs
    Comparison=ComparisonA=ComparisonB=NULL

    es.design <- stats::model.matrix(~0 + Comparison, data = pData(es.copy))

    fit <- lmFit(es.copy, es.design)

    A <- NULL; B <- NULL
    fit2 <- contrasts.fit(fit, makeContrasts(ComparisonB - ComparisonA, levels = es.design))
    fit2 <- eBayes(fit2)
    de <- topTable(fit2, adjust.method = "BH", number = Inf)
    de <- de[row.names(fData(es.copy)), ]
    de
}

#' Differential Expression analysis.
#'
#' \code{limmaAnalysis} performs differential expression analysis
#'     from limma package and returns a ProtoBuf-serialized resulting
#'     de-matrix.
#'
#' @param es ExpressionSet object. It should be normalized for
#'     more accurate analysis.
#'
#' @param fieldValues Vector of comparison values, mapping
#'     categories' names to columns/samples
#'
#' @return Name of the file containing serialized de-matrix.
#'
#' @import Biobase
#' @import limma
#'
#' @examples
#' \dontrun{
#' data(es)
#' limmaAnalysis(es, fieldValues = c("A", "A", "A", "B", "B"))
#' }
limmaAnalysis <- function(es, fieldValues) {
    fieldValues <- replace(fieldValues, fieldValues == "", NA)
    de <- limmaAnalysisImpl(es, fieldValues)

    toRemove <- intersect(colnames(fData(es)), colnames(de))
    fData(es)[, toRemove] <- NULL
    fData(es) <- cbind(fData(es), de)
    es$Comparison <- fieldValues
    assign("es", es, envir = parent.frame())

    f <- tempfile(pattern = "de", tmpdir = getwd(), fileext = ".bin")
    writeBin(protolite::serialize_pb(as.list(de)), f)
    jsonlite::toJSON(f)
}

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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