diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 168 |
1 files changed, 160 insertions, 8 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 17c85fe512..ae8e9c5a47 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2230,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.13.2") + (version "5.6.13.3") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m")))) + "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") @@ -5851,14 +5851,14 @@ functions.") (define-public r-rjags (package (name "r-rjags") - (version "4-8") + (version "4-9") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 - "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m")))) + "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a")))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,r-coda))) @@ -6823,13 +6823,13 @@ and coverage methods to tune the choice of threshold.") (define-public r-ggstance (package (name "r-ggstance") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 - (base32 "078ih9s5b0xzf582qg0vjnxvg5qad5ms1v2vdd062ckahi8zz1r8")))) + (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -14752,14 +14752,14 @@ into R and converted to @code{BibEntry} objects.") (define-public r-citr (package (name "r-citr") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "citr" version)) (sha256 (base32 - "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc")))) + "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -14945,3 +14945,155 @@ path of values for the regularization parameter.") library uses. It is also possible to control the number of threads in OpenMP.") (license license:agpl3+))) + +(define-public r-lda + (package + (name "r-lda") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "lda" version)) + (sha256 + (base32 + "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/lda/") + (synopsis "Collapsed Gibbs sampling methods for topic models") + (description + "This package implements @dfn{latent Dirichlet allocation} (LDA) and +related models. This includes (but is not limited to) sLDA, corrLDA, and the +mixed-membership stochastic blockmodel. Inference for all of these models is +implemented via a fast collapsed Gibbs sampler written in C. Utility +functions for reading/writing data typically used in topic models, as well as +tools for examining posterior distributions are also included.") + ;; Any version of the LGPL + (license license:lgpl3+))) + +(define-public r-rann-l1 + (package + (name "r-rann-l1") + (version "2.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "RANN.L1" version)) + (sha256 + (base32 + "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) + (properties `((upstream-name . "RANN.L1"))) + (build-system r-build-system) + (home-page "https://github.com/jefferis/RANN/tree/master-L1") + (synopsis "Fast nearest neighbour search using L1 metric") + (description + "This package provides tools to find the k nearest neighbours for every +point in a given dataset in O(N log N) time using Arya and Mount's ANN +library. There is support for approximate as well as exact searches, fixed +radius searches and @code{bd} as well as @code{kd} trees. The distance is +computed using the L1 (Manhattan, taxicab) metric.") + (license license:gpl3+))) + +(define-public r-patchwork + ;; There has been no public release yet. + (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") + (revision "1")) + (package + (name "r-patchwork") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/thomasp85/patchwork.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable))) + (home-page "https://github.com/thomasp85/patchwork") + (synopsis "Compose ggplot2 plots") + (description + "The @code{ggplot2} package provides a strong API for sequentially +building up a plot, but does not concern itself with composition of multiple +plots. Patchwork is a package that expands the API to allow for arbitrarily +complex composition of plots by providing mathmatical operators for combining +multiple plots.") + (license license:expat)))) + +(define-public r-liger + (package + (name "r-liger") + (version "0.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MacoskoLab/liger.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file "inst/java/ModularityOptimizer.jar") + #t)))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-java-part + (lambda* (#:key inputs #:allow-other-keys) + (invoke "unzip" (assoc-ref inputs "optimizer-src")) + (for-each (lambda (file) (invoke "javac" file)) + (find-files "." "\\.java$")) + (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" + (find-files "." "\\.class$")) + #t))))) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-hmisc" ,r-hmisc) + ("r-ica" ,r-ica) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-mclust" ,r-mclust) + ("r-patchwork" ,r-patchwork) + ("r-plyr" ,r-plyr) + ("r-rann-l1" ,r-rann-l1) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-riverplot" ,r-riverplot) + ("r-rtsne" ,r-rtsne) + ("r-snow" ,r-snow))) + (native-inputs + `(("jdk" ,icedtea "jdk") + ;; See https://github.com/MacoskoLab/liger/issues/96 + ;; The optimizer is released under the Expat license. + ("optimizer-src" + ,(origin + (method url-fetch) + (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip") + (sha256 + (base32 + "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) + ("unzip" ,unzip) + ("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/MacoskoLab/liger") + (synopsis "Integrate and analyze multiple single-cell datasets") + (description + "LIGER is a package for integrating and analyzing multiple single-cell +datasets, developed and maintained by the Macosko lab. It relies on +integrative non-negative matrix factorization to identify shared and +dataset-specific factors.") + (license license:gpl3))) |