@@ 11535,6 11535,71 @@ including:
dynamic cellular processes at single-cell resolution.")
(license license:expat))))
+;; Needed for r-liana
+(define-public r-omnipathr/devel
+ (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a")
+ (revision "1"))
+ (package
+ (name "r-omnipathr")
+ (version (git-version "3.5.5" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/saezlab/omnipathr")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq"))))
+ (properties `((upstream-name . "OmnipathR")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list r-checkmate
+ r-crayon
+ r-curl
+ r-digest
+ r-dplyr
+ r-httr
+ r-igraph
+ r-jsonlite
+ r-later
+ r-logger
+ r-magrittr
+ r-progress
+ r-purrr
+ r-rappdirs
+ r-readr
+ r-readxl
+ r-rlang
+ r-rvest
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect
+ r-withr
+ r-xml2
+ r-yaml))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/saezlab/omnipathr")
+ (synopsis "OmniPath web service client and more")
+ (description
+ "This package provides a client for the OmniPath web service and many
+other resources. It also includes functions to transform and pretty print
+some of the downloaded data, functions to access a number of other resources
+such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to
+Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology,
+InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015,
+RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore,
+OmnipathR features a close integration with the NicheNet method for ligand
+activity prediction from transcriptomics data, and its R implementation
+@code{nichenetr}.")
+ (license license:expat))))
+
(define-public r-circus
(package
(name "r-circus")