diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 42 | ||||
| -rw-r--r-- | gnu/packages/cran.scm | 27 | ||||
| -rw-r--r-- | gnu/packages/llvm.scm | 10 |
3 files changed, 78 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59b921af82..4d3f86bfd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5111,6 +5111,48 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +(define-public r-scmap + (package + (name "r-scmap") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scmap" version)) + (sha256 + (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (properties `((upstream-name . "scmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hemberg-lab/scmap") + (synopsis "Tool for unsupervised projection of single cell RNA-seq data") + (description + "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the +composition of complex tissues since the technology allows researchers to +define cell-types using unsupervised clustering of the transcriptome. +However, due to differences in experimental methods and computational +analyses, it is often challenging to directly compare the cells identified in +two different experiments. @code{scmap} is a method for projecting cells from +a scRNA-seq experiment onto the cell-types or individual cells identified in a +different experiment.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61a1b055b9..5a8285b342 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -425,6 +425,33 @@ Distance (EMD).") (description "This package lets you manage Google Drive files from R.") (license license:expat))) +(define-public r-googlevis + (package + (name "r-googlevis") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "googleVis" version)) + (sha256 + (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz")))) + (properties `((upstream-name . "googleVis"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite)) + (native-inputs (list r-knitr)) + (home-page "https://mages.github.io/googleVis/") + (synopsis "R interface to Google Charts") + (description + "The @code{googleVis} package provides an interface between R and the Google +Charts API. Google Charts offer interactive charts which can be embedded into +web pages. The functions of the @code{googleVis} package allow the user to +visualise data stored in R data frames with Google Charts without uploading +the data to Google. The output of a @code{googleVis} function is HTML code +that contains the data and references to JavaScript functions hosted by +Google. @code{googleVis} makes use of the internal R HTTP server to display +the output locally.") + (license license:gpl2+))) + (define-public r-guix-install (package (name "r-guix-install") diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index aedf039ff4..d3b16f2759 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -216,7 +216,15 @@ given PATCHES. When TOOLS-EXTRA is given, it must point to the ;; Use a sane default include directory. (string-append "-DC_INCLUDE_DIRS=" (assoc-ref %build-inputs "libc") - "/include")) + "/include") + ,@(if (target-riscv64?) + (list "-DLIBOMP_LIBFLAGS=-latomic" + "-DCMAKE_SHARED_LINKER_FLAGS=-latomic") + `())) + + ,@(if (target-riscv64?) + `(#:make-flags '("LDFLAGS=-latomic")) + '()) ;; Don't use '-g' during the build to save space. #:build-type "Release" |