diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 44 | ||||
| -rw-r--r-- | gnu/packages/browser-extensions.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/chromium.scm | 8 | ||||
| -rw-r--r-- | gnu/packages/cran.scm | 26 | ||||
| -rw-r--r-- | gnu/packages/llvm.scm | 10 |
5 files changed, 81 insertions, 11 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 75d2b97bba..9788285707 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2188,6 +2188,50 @@ set analyses, and can deal with repeated or longitudinal data.") biological sequences.") (license license:gpl3))) +(define-public r-deconvr + (package + (name "r-deconvr") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deconvR" version)) + (sha256 + (base32 + "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + (properties `((upstream-name . "deconvR"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocgenerics + r-data-table + r-dplyr + r-e1071 + r-foreach + r-genomicranges + r-iranges + r-magrittr + r-mass + r-matrixstats + r-methylkit + r-nnls + r-quadprog + r-rsq + r-s4vectors + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/BIMSBbioinfo/deconvR") + (synopsis "Simulation and deconvolution of omic profiles") + (description + "This package provides a collection of functions designed for analyzing +deconvolution of the bulk sample(s) using an atlas of reference omic signature +profiles and a user-selected model. Users are given the option to create or +extend a reference atlas and,also simulate the desired size of the bulk +signature profile of the reference cell types. The package includes the +cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can +be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to +make mapping WGBS data to their probe IDs easier.") + (license license:artistic2.0))) + (define-public r-decoupler (package (name "r-decoupler") diff --git a/gnu/packages/browser-extensions.scm b/gnu/packages/browser-extensions.scm index f305552076..1012e4b643 100644 --- a/gnu/packages/browser-extensions.scm +++ b/gnu/packages/browser-extensions.scm @@ -51,7 +51,7 @@ supported content to the Kodi media center.") (define ublock-origin (package (name "ublock-origin") - (version "1.42.4") + (version "1.43.0") (home-page "https://github.com/gorhill/uBlock") (source (origin (method git-fetch) @@ -62,7 +62,7 @@ supported content to the Kodi media center.") (file-name (git-file-name name version)) (sha256 (base32 - "1is55pxnlylcr1pfigwgfn7kcx1rapy1cafdh6g83bdhscgh75g3")))) + "0w0by41v1s1cbd3bfjlb7kxr2bl6r5z3jvizlx02x14hqlppma9k")))) (build-system gnu-build-system) (outputs '("xpi" "firefox" "chromium")) (arguments diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 5936ab23c3..bdfebed99e 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -312,8 +312,8 @@ ;; run the Blink performance tests, just remove everything to save ~70MiB. '("third_party/blink/perf_tests")) -(define %chromium-version "102.0.5005.61") -(define %ungoogled-revision (string-append %chromium-version "-3")) +(define %chromium-version "102.0.5005.115") +(define %ungoogled-revision (string-append %chromium-version "-1")) (define %debian-revision "debian/102.0.5005.61-1") (define %ungoogled-origin @@ -324,7 +324,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "19i4ygxjm503dmck3bdqv3fcpda3dp9wr7z306pi6i1k989rbs8l")))) + "1z2xkxxviggyyksga74cqa4v73gynlgzi22ckg8yv84qxrklik6p")))) (define %debian-origin (origin @@ -477,7 +477,7 @@ %chromium-version ".tar.xz")) (sha256 (base32 - "07vbi3gn9g4n04b2qi2hm34r122snrqaifa46yk3pyh1d79rfdqs")) + "1rj7vy824vn513hiivc90lnxvxyi2s0qkdmfqsdssv9v6zjl079h")) (modules '((guix build utils))) (snippet (force ungoogled-chromium-snippet)))) (build-system gnu-build-system) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c1f0dc08b7..179616b43d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31617,6 +31617,32 @@ asynchronously from formatting.") utility operations.") (license license:gpl3))) +(define-public r-rsq + (package + (name "r-rsq") + (version "2.5") + (source (origin + (method url-fetch) + (uri (cran-uri "rsq" version)) + (sha256 + (base32 + "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f")))) + (properties `((upstream-name . "rsq"))) + (build-system r-build-system) + (propagated-inputs + (list r-deriv + r-lme4 + r-mass + r-matrix + r-nlme)) + (home-page "https://cran.r-project.org/package=rsq") + (synopsis "R-squared and related measures") + (description + "Calculate generalized R-squared, partial R-squared, and partial correlation +coefficients for generalized linear (mixed) models (including quasi models +with well defined variance functions).") + (license license:gpl2))) + (define-public r-webutils (package (name "r-webutils") diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 8bc9e8904c..c66714a097 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -541,10 +541,10 @@ output), and Binutils.") ("libc-static" ,glibc "static"))))) (define %llvm-monorepo-hashes - '(("14.0.4" . "1y4yvx749cn3gkpc9kf48xbd2wc2lry8x5zdpk3sbrkqs8vrji4q"))) + '(("14.0.5" . "1hdv020x4k5fp38hik3bxz8k2sr3gnyj9iym3yhjhwygzgwgxjh9"))) (define %llvm-patches - '(("14.0.4" . ("clang-14.0-libc-search-path.patch")))) + '(("14.0.5" . ("clang-14.0-libc-search-path.patch")))) (define (llvm-monorepo version) (origin @@ -559,7 +559,7 @@ output), and Binutils.") (define-public llvm-14 (package (name "llvm") - (version "14.0.4") + (version "14.0.5") (source (llvm-monorepo version)) (build-system cmake-build-system) (outputs '("out" "opt-viewer")) @@ -647,7 +647,7 @@ of programming tools as well as libraries with equivalent functionality.") (package-version llvm-14))) (sha256 (base32 - "1vcgmvh0r28a1z87p3y4h2326zi8liq7l9mcfvmx22x9bmbcpfn8")))))) + "1p9y5fbcw3ynb79nzyadirwdla03bq38k6d9nhv9x8z2q4ypsga4")))))) (package (inherit template) (arguments @@ -1176,7 +1176,7 @@ of programming tools as well as libraries with equivalent functionality.") (define-public lld-14 (package (name "lld") - (version "14.0.4") + (version "14.0.5") (source (llvm-monorepo version)) (build-system cmake-build-system) (inputs |