;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
(define-public r-rticles
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
- (version "0.3.5")
+ (version "0.3.6")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
- "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
+ "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
+ ("r-glue" ,r-glue)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
(define-public r-callr
(package
(name "r-callr")
- (version "3.4.3")
+ (version "3.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
+ "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
(define-public r-jsonlite
(package
(name "r-jsonlite")
- (version "1.7.0")
+ (version "1.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "jsonlite" version))
(sha256
(base32
- "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
+ "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-hardhat
(package
(name "r-hardhat")
- (version "0.1.3")
+ (version "0.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "hardhat" version))
(sha256
(base32
- "10x8fw0skaqci03v2qqpbradbra9arm3s5pskcwm4wricd2imr40"))))
+ "0gaj4hr4dj27jaasp7v0hzaivipplvq746ajsyz4yd1in03hfjvs"))))
(properties `((upstream-name . "hardhat")))
(build-system r-build-system)
(propagated-inputs
value.")
(license license:gpl3)))
+(define-public r-adaptivesparsity
+ (package
+ (name "r-adaptivesparsity")
+ (version "1.6")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "AdaptiveSparsity" version))
+ (sha256
+ (base32
+ "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
+ (properties
+ `((upstream-name . "AdaptiveSparsity")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'link-against-armadillo
+ (lambda _
+ (substitute* "src/Makevars"
+ (("PKG_LIBS=" prefix)
+ (string-append prefix "-larmadillo")))
+ #t)))))
+ (propagated-inputs
+ `(("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (inputs
+ `(("armadillo" ,armadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
+ (synopsis "Adaptive sparsity models")
+ (description
+ "This package implements the Figueiredo machine learning algorithm for
+adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
+geometric models.")
+ (license license:lgpl3+)))
+
+(define-public r-diffusionmap
+ (package
+ (name "r-diffusionmap")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diffusionMap" version))
+ (sha256
+ (base32
+ "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
+ (properties `((upstream-name . "diffusionMap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-scatterplot3d" ,r-scatterplot3d)))
+ (home-page "https://www.r-project.org")
+ (synopsis "Diffusion map")
+ (description "This package implements the diffusion map method of data
+parametrization, including creation and visualization of diffusion maps,
+clustering with diffusion K-means and regression using the adaptive regression
+model.")
+ (license license:gpl2)))
+
+(define-public r-igraph
+ (package
+ (name "r-igraph")
+ (version "1.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "igraph" version))
+ (sha256
+ (base32
+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("gmp" ,gmp)
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-pkgconfig" ,r-pkgconfig)))
+ (home-page "https://igraph.org")
+ (synopsis "Network analysis and visualization")
+ (description
+ "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+ (license license:gpl2+)))
+
(define-public r-workflows
(package
(name "r-workflows")
- (version "0.1.1")
+ (version "0.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "workflows" version))
(sha256
(base32
- "14lzbszz7ybfzqa5zw1hfh81b8rbwwyza6x8nhpnknl6x4adqfql"))))
+ "1d5njd1xdl8kghlbar4acgl9hxq83p6k7yks592cvakmcz7f853m"))))
(properties `((upstream-name . "workflows")))
(build-system r-build-system)
(propagated-inputs
(define-public r-yardstick
(package
(name "r-yardstick")
- (version "0.0.6")
+ (version "0.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "yardstick" version))
(sha256
(base32
- "1qkvbvc0cnwl5mkk47swnd8by84zz0qpy1996fziapn35qxvx9qa"))))
+ "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
(properties `((upstream-name . "yardstick")))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
("r-generics" ,r-generics)
("r-proc" ,r-proc)
- ("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)
("r-tidyselect" ,r-tidyselect)))
(native-inputs
(define-public r-dials
(package
(name "r-dials")
- (version "0.0.7")
+ (version "0.0.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "dials" version))
(sha256
(base32
- "0fqxdlgwdwpmni2760yagrzqbniz72yl547fcmlx9kzazhzszgq0"))))
+ "0jxmlcy20y57chflx91fqz6c4pbdckzr7jirq4s72vp723avrr4p"))))
(properties `((upstream-name . "dials")))
(build-system r-build-system)
(propagated-inputs
(define-public r-tune
(package
(name "r-tune")
- (version "0.1.0")
+ (version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tune" version))
(sha256
(base32
- "0xiidzkl0hbd0f7jh1v2kkg26wdgy33w74c9bmpjgy317ckhsz8h"))))
+ "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
(properties `((upstream-name . "tune")))
(build-system r-build-system)
(propagated-inputs
("r-rsample" ,r-rsample)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)
("r-workflows" ,r-workflows)
("r-yardstick" ,r-yardstick)))
(home-page "https://github.com/tidymodels/tune")
(define-public r-tidypredict
(package
(name "r-tidypredict")
- (version "0.4.5")
+ (version "0.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidypredict" version))
(sha256
(base32
- "1i6zl6wjz6wbpkmkc9z9ikp8zgck3qh38lar0r6q2jzl8fxpimg4"))))
+ "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
(properties `((upstream-name . "tidypredict")))
(build-system r-build-system)
(propagated-inputs
(define-public r-tidytext
(package
(name "r-tidytext")
- (version "0.2.4")
+ (version "0.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytext" version))
(sha256
(base32
- "0gck3f039qkpkwn92jlyfan76w0xydg17bh6nsg9qlba7c35kzs6"))))
+ "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
(properties `((upstream-name . "tidytext")))
(build-system r-build-system)
(propagated-inputs
("r-matrix" ,r-matrix)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
- ("r-stopwords" ,r-stopwords)
("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
("r-tokenizers" ,r-tokenizers)))
(native-inputs
`(("r-knitr" ,r-knitr)))
"This is a package for text mining for word processing and sentiment
analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
(license license:expat)))
+
+(define-public r-parsnip
+ (package
+ (name "r-parsnip")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "parsnip" version))
+ (sha256
+ (base32
+ "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
+ (properties `((upstream-name . "parsnip")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
+ ("r-globals" ,r-globals)
+ ("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
+ ("r-prettyunits" ,r-prettyunits)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://parsnip.tidymodels.org")
+ (synopsis "Common API to modeling and analysis functions")
+ (description
+ "This package provides a common interface to allow users to specify a
+model without having to remember the different argument names across different
+functions or computational engines (e.g. R, Spark, Stan, etc).")
+ (license license:gpl2)))
+
+(define-public r-infer
+ (package
+ (name "r-infer")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "infer" version))
+ (sha256
+ (base32
+ "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
+ (properties `((upstream-name . "infer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-glue" ,r-glue)
+ ("r-magrittr" ,r-magrittr)
+ ("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tidymodels/infer")
+ (synopsis "Tidy statistical inference")
+ (description
+ "The objective of this package is to perform inference using an
+expressive statistical grammar that coheres with the Tidy design framework.")
+ (license license:cc0)))
+
+(define-public r-modeldata
+ (package
+ (name "r-modeldata")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "modeldata" version))
+ (sha256
+ (base32
+ "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
+ (properties `((upstream-name . "modeldata")))
+ (build-system r-build-system)
+ (home-page "https://modeldata.tidymodels.org")
+ (synopsis "Data sets useful for modeling packages")
+ (description
+ "This package provides data sets used for demonstrating or testing
+model-related packages.")
+ (license license:expat)))
+
+(define-public r-tidymodels
+ (package
+ (name "r-tidymodels")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidymodels" version))
+ (sha256
+ (base32
+ "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
+ (properties `((upstream-name . "tidymodels")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-broom" ,r-broom)
+ ("r-cli" ,r-cli)
+ ("r-crayon" ,r-crayon)
+ ("r-dials" ,r-dials)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-infer" ,r-infer)
+ ("r-magrittr" ,r-magrittr)
+ ("r-modeldata" ,r-modeldata)
+ ("r-parsnip" ,r-parsnip)
+ ("r-purrr" ,r-purrr)
+ ("r-recipes" ,r-recipes)
+ ("r-rlang" ,r-rlang)
+ ("r-rsample" ,r-rsample)
+ ("r-rstudioapi" ,r-rstudioapi)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tune" ,r-tune)
+ ("r-workflows" ,r-workflows)
+ ("r-yardstick" ,r-yardstick)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
+ (home-page "https://github.com/tidymodels/tidymodels")
+ (synopsis "Tidy collection for modeling and statistical analysis")
+ (description
+ "The tidy modeling \"verse\" is a collection of packages for modeling and
+statistical analysis that share the underlying design philosophy, grammar, and
+data structures of the tidyverse.")
+ (license license:gpl3)))
+
+(define-public r-mlecens
+ (package
+ (name "r-mlecens")
+ (version "0.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MLEcens" version))
+ (sha256
+ (base32
+ "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
+ (properties `((upstream-name . "MLEcens")))
+ (build-system r-build-system)
+ (home-page "http://stat.ethz.ch/~maathuis/")
+ (synopsis "Computation of the MLE for bivariate (interval) censored data")
+ (description
+ "This package contains functions to compute the nonparametric
+@dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
+@code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
+To be more precise, we consider the situation where we observe a set of
+rectangles that are known to contain the unobservable realizations of (X,Y).
+We compute the MLE based on such a set of rectangles. The methods can also be
+used for univariate censored data (see data set @code{cosmesis}), and for
+censored data with competing risks (see data set @code{menopause}). The
+package also provides functions to visualize the observed data and the MLE.")
+ (license license:gpl2+)))
+
+(define-public r-perm
+ (package
+ (name "r-perm")
+ (version "1.0-0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "perm" version))
+ (sha256
+ (base32
+ "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
+ (properties `((upstream-name . "perm")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/perm/")
+ (synopsis "Exact or asymptotic permutation tests")
+ (description
+ "This package provides several methods for performing permutation tests.
+It has three main functions, to perform linear permutation tests. These tests
+are tests where the test statistic is the sum of the product of a
+covariate (usually group indicator) and the scores.")
+ ;; Any version of the GPL
+ (license license:gpl2+)))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.46-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl" version))
+ (sha256
+ (base32
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
+ (build-system r-build-system)
+ (home-page "https://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics system.
+It is used to analyze experimental crosses for identifying genes contributing
+to variation in quantitative traits (so-called quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl estimates genetic maps, to identify
+genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
+genome scans.")
+ (license license:gpl3)))
+
+(define-public r-qtl2
+ (package
+ (name "r-qtl2")
+ (version "0.22-11")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://kbroman.org/qtl2/")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
+ (description
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
+ (license license:gpl3)))
+
+(define-public r-seqminer
+ (package
+ (name "r-seqminer")
+ (version "8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "seqminer" version))
+ (sha256
+ (base32
+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://seqminer.genomic.codes")
+ (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+ (description
+ "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+ ;; Any version of the GPL is acceptable
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-maldiquant
+ (package
+ (name "r-maldiquant")
+ (version "1.19.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MALDIquant" version))
+ (sha256
+ (base32
+ "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
+ (properties `((upstream-name . "MALDIquant")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/MALDIquant")
+ (synopsis "Quantitative analysis of mass spectrometry data")
+ (description
+ "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data. In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+ (license license:gpl3+)))
+
+(define-public r-seurat
+ (package
+ (name "r-seurat")
+ (version "3.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-cluster" ,r-cluster)
+ ("r-cowplot" ,r-cowplot)
+ ("r-fitdistrplus" ,r-fitdistrplus)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggridges" ,r-ggridges)
+ ("r-httr" ,r-httr)
+ ("r-ica" ,r-ica)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-leiden" ,r-leiden)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-miniui" ,r-miniui)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plotly" ,r-plotly)
+ ("r-png" ,r-png)
+ ("r-rann" ,r-rann)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rlang" ,r-rlang)
+ ("r-rocr" ,r-rocr)
+ ("r-rsvd" ,r-rsvd)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-sctransform" ,r-sctransform)
+ ("r-shiny" ,r-shiny)
+ ("r-spatstat" ,r-spatstat)
+ ("r-tibble" ,r-tibble)
+ ("r-uwot" ,r-uwot)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data. It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+ (license license:gpl3)))
+
+(define-public r-phangorn
+ (package
+ (name "r-phangorn")
+ (version "2.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phangorn" version))
+ (sha256
+ (base32
+ "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/KlausVigo/phangorn")
+ (synopsis "Phylogenetic analysis in R")
+ (description
+ "Phangorn is a package for phylogenetic analysis in R. It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+ (license license:gpl2+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-subplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))
+
+(define-public r-absfiltergsea
+ (package
+ (name "r-absfiltergsea")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AbsFilterGSEA" version))
+ (sha256
+ (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+ (properties `((upstream-name . "AbsFilterGSEA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq" ,r-deseq)
+ ("r-limma" ,r-limma)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+ (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+ (description
+ "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+ Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+ (license license:gpl2)))
HCoop / jackhill / guix / guix.git / blobdiff