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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=PfUVJ09q; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.11 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=PfUVJ09q; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 40D5F150F0 X-Spam-Score: 7.11 X-Migadu-Scanner: scn1.migadu.com X-TUID: FVAHVluVd0AA * gnu/packages/bioconductor.scm (r-aldex2): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..3abd57359d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,48 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aldex2 + (package + (name "r-aldex2") + (version "1.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ALDEx2" version)) + (sha256 + (base32 + "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + (properties `((upstream-name . "ALDEx2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ggloor/ALDEx_bioc") + (synopsis + "Analysis Of differential abundance taking sample variation into account") + (description + "This package provides a differential abundance analysis for the comparison +of two or more conditions. Useful for analyzing data from standard RNA-seq or +meta-RNA-seq assays as well as selected and unselected values from in-vitro +sequence selections. Uses a Dirichlet-multinomial model to infer abundance from +counts, optimized for three or more experimental replicates. The method infers +biological and sampling variation to calculate the expected false discovery +rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test +(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear +model (via aldex.glm), or a correlation test (via aldex.corr). All tests report +p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates +expected standardized effect sizes for paired or unpaired study designs.") + ;; The code for the function "rdirichlet" which is from the "R" package + ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball + ;; LICENSE specifies GPL-3. + (license (list license:agpl3+ license:gpl2+ license:gpl3)))) + (define-public r-aneufinder (package (name "r-aneufinder") -- 2.36.1