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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=NBZXDrOb; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (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: 5.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=NBZXDrOb; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (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: 052DDC15C X-Spam-Score: 5.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: WvWTYxqXIF9t * gnu/packages/bioconductor.scm (r-pscbs): 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 80cf28c954..7fed1aa18b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4560,6 +4560,48 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of Parent-Specific DNA Copy Numbers") + (description + "Segmentation of allele-specific DNA copy number data and detection of +regions with abnormal copy number within each parental chromosome. Both +tumor-normal paired and tumor-only analyses are supported.") + (license license:gpl2+))) + (define-public r-protgenerics (package (name "r-protgenerics") base-commit: 01793ed03e8aa0960bff7adc21fd270e1527e68e -- 2.36.0