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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=hRt2dxw8; 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: 8.69 X-Spam: Yes Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=hRt2dxw8; 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: 964F12CCCE X-Spam-Score: 8.69 X-Migadu-Spam: Yes X-Migadu-Scanner: scn1.migadu.com X-TUID: JfEJtV51svqV * gnu/packages/bioconductor.scm (r-debcam): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8535250f9..994b3b0137 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -48,6 +48,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -3051,6 +3052,45 @@ (define-public r-dearseq set analyses, and can deal with repeated or longitudinal data.") (license license:gpl2))) +(define-public r-debcam + (package + (name "r-debcam") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "debCAM" version)) + (sha256 + (base32 + "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + (properties `((upstream-name . "debCAM"))) + (build-system r-build-system) + (inputs (list openjdk)) + (propagated-inputs + (list r-apcluster + r-biobase + r-biocparallel + r-corpcor + r-dmwr2 + r-geometry + r-nmf + r-nnls + r-pcapp + r-rjava + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/debCAM") + (synopsis "Deconvolution by convex analysis of mixtures") + (description + "This package is an R implementation for fully unsupervised deconvolution +of complex tissues. @code{DebCAM} provides basic functions to perform unsupervised +deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis +of Mixtures} and some auxiliary functions to help understand the subpopulation- +specific results. It also implements functions to perform supervised deconvolution +based on prior knowledge of molecular markers, S matrix or A matrix. Combining +molecular markers from CAM and from prior knowledge can achieve semi-supervised +deconvolution of mixtures.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher") -- 2.38.0