[bug#64250] [PATCH 00/15] *** R package (scriabin) ***

[bug#64250] [PATCH 00/15] *** R package (scriabin) ***

[Navid Afkhami]

Hi,

An R package + all the dependencies.

Your review is highly appreciated.

Thank you

Navid Afkhami (15):
  gnu: Add r-paramhelpers.
  gnu: Add r-smoof.
  gnu: Add r-parallelmap.
  gnu: Add r-mlr.
  gnu: Add r-mlrmbo.
  gnu: Add r-emoa.
  gnu: Add r-diagrammer.
  gnu: Add r-tidyft.
  gnu: Add r-ggfittext.
  gnu: Add r-dunn-test.
  gnu: Add r-cellid.
  gnu: Add r-dicekriging.
  gnu: Add r-nichenetr.
  gnu: Add r-fsa.
  gnu: Add r-scriabin.

 gnu/packages/bioconductor.scm   |  44 +++++
 gnu/packages/bioinformatics.scm | 111 +++++++++++
 gnu/packages/cran.scm           | 318 ++++++++++++++++++++++++++++++++
 3 files changed, 473 insertions(+)


base-commit: f25529b08e356f89ca7cecc44295085531a8faba
-- 
2.34.1

[bug#64250] [PATCH 01/15] gnu: Add r-paramhelpers.

[Navid Afkhami]

* gnu/packages/cran.scm (r-paramhelpers): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ba81580258..d9a1914eb0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2408,6 +2408,29 @@ (define-public r-paralleldist
 naming conventions as distance methods of existing R packages.")
     (license license:gpl2+)))
 
+(define-public r-paramhelpers
+  (package
+    (name "r-paramhelpers")
+    (version "1.14.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ParamHelpers" version))
+              (sha256
+               (base32
+                "088sl3az4ysq8cyw82brdn9xm5yy7rqskxih462d1m5hi62gyl04"))))
+    (properties `((upstream-name . "ParamHelpers")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-backports r-bbmisc r-checkmate r-fastmatch))
+    (home-page "https://paramhelpers.mlr-org.com")
+    (synopsis
+     "Helpers for parameters in black-box ptimization, tuning and machine learning")
+    (description
+     "Package for parameter description and operations in optimization, tuning and machine learning.
+Parameters can be described (type, constraints, defaults, etc.), combined
+to parameter sets and can in general be programmed on.  A useful OptPath
+object (archive) to log function evaluations is also provided.")
+    (license license:bsd-2)))
+
 (define-public r-pheatmap
   (package
     (name "r-pheatmap")
-- 
2.34.1

[bug#64250] [PATCH 02/15] gnu: Add r-smoof.

[Navid Afkhami]

* gnu/packages/cran.scm (r-smoof): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d9a1914eb0..3eec62f9c2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8159,6 +8159,34 @@ (define-public r-sm
 and density estimation")
     (license license:gpl2+)))
 
+(define-public r-smoof
+  (package
+    (name "r-smoof")
+    (version "1.6.0.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "smoof" version))
+              (sha256
+               (base32
+                "1cazhnd0m5jjzixaqgqh2h3rsa2sw3k8slj5cmgm8v47aaqn91mg"))))
+    (properties `((upstream-name . "smoof")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbmisc
+                             r-checkmate
+                             r-ggplot2
+                             r-paramhelpers
+                             r-rcpp
+                             r-rcpparmadillo))
+    (home-page "https://jakobbossek.github.io/smoof/")
+    (synopsis "Single and multi-objective optimization test functions")
+    (description
+     "This tool generates high number of both single- and multi-objective test functions.
+These functions are frequently used for the benchmarking of
+(numerical) optimization algorithms.  Moreover, it offers a
+set of convenient functions to generate, plot and work with
+objective functions.")
+    (license license:bsd-2)))
+
 (define-public r-smurf
   (package
     (name "r-smurf")
-- 
2.34.1

[bug#64250] [PATCH 03/15] gnu: Add r-parallelmap.

[Navid Afkhami]

* gnu/packages/cran.scm (r-parallelmap): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3eec62f9c2..7deebbe72f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2431,6 +2431,30 @@ (define-public r-paramhelpers
 object (archive) to log function evaluations is also provided.")
     (license license:bsd-2)))
 
+(define-public r-parallelmap
+  (package
+    (name "r-parallelmap")
+    (version "1.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "parallelMap" version))
+              (sha256
+               (base32
+                "1qg7zpz5sd9jp8wzjqahkhipwj1jn192llwg06q4gv9mlcsac261"))))
+    (properties `((upstream-name . "parallelMap")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bbmisc r-checkmate))
+    (home-page "https://parallelmap.mlr-org.com")
+    (synopsis "Unified interface to parallelization back-ends")
+    (description
+     "Unified parallelization framework for multiple back-end.
+This package is designed for internal package and interactive usage.
+The main operation is parallel mapping over lists.  Supports local',
+multicore', mpi and BatchJobs mode.  Allows tagging of the parallel
+operation with a level name that can be later selected by the user to
+switch on parallel execution for exactly this operation.")
+    (license license:bsd-2)))
+
 (define-public r-pheatmap
   (package
     (name "r-pheatmap")
-- 
2.34.1

[bug#64250] [PATCH 04/15] gnu: Add r-mlr.

[Navid Afkhami]

* gnu/packages/cran.scm (r-mlr): New variable.
---
 gnu/packages/cran.scm | 47 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7deebbe72f..0fa8680e9c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -35206,6 +35206,53 @@ (define-public r-mhg
 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
     (license license:gpl2)))
 
+(define-public r-mlr
+  (package
+    (name "r-mlr")
+    (version "2.19.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "mlr" version))
+              (sha256
+               (base32
+                "00jjhvaqifj6glqsyzixlp56bvlch5smck8kk3klcmwx9pasyllx"))))
+    (properties `((upstream-name . "mlr")))
+    (build-system r-build-system)
+    (inputs (list gdal
+                  geos
+                  glu
+                  gmp
+                  gsl
+                  jags
+                  mpfr
+                  openmpi
+                  proj
+                  udunits))
+    (propagated-inputs (list r-backports
+                             r-bbmisc
+                             r-checkmate
+                             r-data-table
+                             r-ggplot2
+                             r-parallelmap
+                             r-paramhelpers
+                             r-stringi
+                             r-survival
+                             r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://mlr.mlr-org.com")
+    (synopsis "Machine learning in R")
+    (description
+     "Interface to a large number of classification and regression techniques.
+These technics include machine-readable parameter descriptions.  There is also
+an experimental extension for survival analysis, clustering and general,
+example-specific cost-sensitive learning.  Generic resampling, including
+cross-validation, bootstrapping and subsampling.  Hyperparameter tuning with
+modern optimization techniques, for single- and multi-objective problems.
+Filter and wrapper methods for feature selection.  Extension of basic learners
+with additional operations common in machine learning, also allowing for easy
+nested resampling.  Most operations can be parallelized.")
+    (license license:bsd-2)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.34.1

[bug#64250] [PATCH 05/15] gnu: Add r-mlrmbo.

[Navid Afkhami]

* gnu/packages/cran.scm (r-mlrmbo): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0fa8680e9c..4e9ea8b67e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -35253,6 +35253,40 @@ (define-public r-mlr
 nested resampling.  Most operations can be parallelized.")
     (license license:bsd-2)))
 
+(define-public r-mlrmbo
+  (package
+    (name "r-mlrmbo")
+    (version "1.1.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "mlrMBO" version))
+              (sha256
+               (base32
+                "16fwj7m28g4km7yalqppxmh3lw2jln0z072l6awia38qkdg6xwhc"))))
+    (properties `((upstream-name . "mlrMBO")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-backports
+                             r-bbmisc
+                             r-checkmate
+                             r-data-table
+                             r-lhs
+                             r-mlr
+                             r-parallelmap
+                             r-paramhelpers
+                             r-smoof))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mlr-org/mlrMBO")
+    (synopsis "Model-based optimization with mlr")
+    (description
+     "Flexible and comprehensive R toolbox for model-based optimization.
+It implements Efficient Global Optimization Algorithm for single- and
+multi-objective optimization.  Supports mixed parameters.  The machine
+learning toolbox mlr offers regression learners.  Provides various
+infill criteria.  Features batch proposal, parallel execution,
+visualization, logging.  Modular implementation allows easy customization
+by the user.")
+    (license license:bsd-2)))
+
 (define-public r-mlr3measures
   (package
     (name "r-mlr3measures")
-- 
2.34.1

[bug#64250] [PATCH 06/15] gnu: Add r-emoa.

[Navid Afkhami]

* gnu/packages/cran.scm (r-emoa): New variable.
---
 gnu/packages/cran.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4e9ea8b67e..34d4749b14 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26111,6 +26111,24 @@ (define-public r-showtext
 such as Ghostscript is needed to use this package.")
     (license license:asl2.0)))
 
+(define-public r-emoa
+  (package
+    (name "r-emoa")
+    (version "0.5-0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "emoa" version))
+              (sha256
+               (base32
+                "0fr4ia3hkv8c7wkl64a51s6ynldppc812ynwldvbwy25dhlbvs6r"))))
+    (properties `((upstream-name . "emoa")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/emoa/")
+    (synopsis "Evolutionary multiobjective optimization algorithms")
+    (description
+     "Building blocks for the  design and analysis of multiobjective optimization algorithms.")
+    (license license:gpl2)))
+
 (define-public r-emojifont
   (package
     (name "r-emojifont")
-- 
2.34.1

[bug#64250] [PATCH 07/15] gnu: Add r-diagrammer.

[Navid Afkhami]

* gnu/packages/cran.scm (r-diagrammer): New variable.
---
 gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 34d4749b14..247f9a6f96 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -28898,6 +28898,46 @@ (define-public r-diagram
 Francesca Mazzia (2012).")
     (license license:gpl2+)))
 
+(define-public r-diagrammer
+  (package
+    (name "r-diagrammer")
+    (version "1.0.10")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "DiagrammeR" version))
+              (sha256
+               (base32
+                "147q7zgwhd7vc0l134sqkkf6n6s6bznxvcmsrdx2f5df12bsixkj"))))
+    (properties `((upstream-name . "DiagrammeR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-downloader
+                             r-dplyr
+                             r-glue
+                             r-htmltools
+                             r-htmlwidgets
+                             r-igraph
+                             r-magrittr
+                             r-purrr
+                             r-rcolorbrewer
+                             r-readr
+                             r-rlang
+                             r-rstudioapi
+                             r-scales
+                             r-stringr
+                             r-tibble
+                             r-tidyr
+                             r-viridis
+                             r-visnetwork))
+    (native-inputs (list esbuild))
+    (home-page "https://github.com/rich-iannone/DiagrammeR")
+    (synopsis "Graph/network visualization")
+    (description
+     "DiagrammeR creates, modifies, analyzes, and visualizes network graph diagrams.
+The output can be incorporated into R Markdown documents, integrated
+with Shiny web apps, converted to other graph formats, or exported as
+image files.")
+    (license license:expat)))
+
 (define-public r-lim
   (package
     (name "r-lim")
-- 
2.34.1

[bug#64250] [PATCH 08/15] gnu: Add r-tidyft.

[Navid Afkhami]

* gnu/packages/cran.scm (r-tidyft): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 247f9a6f96..9938d07dd9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3005,6 +3005,29 @@ (define-public r-vegan
 data types as well.")
     (license license:gpl2+)))
 
+(define-public r-tidyft
+  (package
+    (name "r-tidyft")
+    (version "0.5.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "tidyft" version))
+              (sha256
+               (base32
+                "00qcsr2sx8fwyil384vgppx0q72qjrkj7h5nv4mdxdi8f9h6ph2r"))))
+    (properties `((upstream-name . "tidyft")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-data-table r-fst r-stringr))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hope-data-science/tidyft")
+    (synopsis "Fast and memory efficient data operations in tidy syntax")
+    (description "Tidyft is an extension of data.table.
+It uses modifiification by reference whenever possible.
+This toolkit is designed for big data analysis in
+high-performance desktop or laptop computers.  The syntax
+of the package is similar or identical to tidyverse.")
+    (license license:expat)))
+
 (define-public r-tidyverse
   (package
     (name "r-tidyverse")
-- 
2.34.1

[bug#64250] [PATCH 09/15] gnu: Add r-ggfittext.

[Navid Afkhami]

* gnu/packages/cran.scm (r-ggfittext): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9938d07dd9..bb09a8d774 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -722,6 +722,26 @@ (define-public r-ggalt
 text annotations.")
     (license license:agpl3)))
 
+(define-public r-ggfittext
+  (package
+    (name "r-ggfittext")
+    (version "0.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ggfittext" version))
+              (sha256
+               (base32
+                "06xfv552nhw13wc8dixyqhhmw5zh8hphrabw090nzb33cpfwzin8"))))
+    (properties `((upstream-name . "ggfittext")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi))
+    (native-inputs (list r-knitr))
+    (home-page "https://wilkox.org/ggfittext/")
+    (synopsis "Ggfittext is a ggplot2 extension for fitting text into boxes")
+    (description
+     "Ggfittext is a ggplot2 extension for fitting text into boxes.")
+    (license license:gpl2)))
+
 (define-public r-glmpca
   (package
     (name "r-glmpca")
-- 
2.34.1

[bug#64250] [PATCH 10/15] gnu: Add r-dunn-test.

[Navid Afkhami]

* gnu/packages/cran.scm (r-dunn-test): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bb09a8d774..2873c3ce10 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -27314,6 +27314,31 @@ (define-public r-dummies
 classes into dummy/indicator variables.")
     (license license:gpl2+)))
 
+(define-public r-dunn-test
+  (package
+    (name "r-dunn-test")
+    (version "1.3.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "dunn.test" version))
+              (sha256
+               (base32
+                "0lqwvyl3pyygfc73nf81gzw3zl3w43r7ki0yw2dgrzhkpb2iji4a"))))
+    (properties `((upstream-name . "dunn.test")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=dunn.test")
+    (synopsis "Dunn's test of multiple comparisons using rank sums")
+    (description
+     "Dunn's test computes stochastic dominance & reports pairwise comparisons.
+This is done following a Kruskal-Wallis test (Kruskal and Wallis, 1952).
+It employs Dunn's z-test-statistic approximations for rank statistics,
+conducting k(k-1)/2 comparisons.  The null hypothesis assumes that the
+probability of a randomly selected value from the first group being
+larger than one from the second group is one half, similar to the
+Wilcoxon-Mann-Whitney test.  Dunn's test serves as a test for median
+difference and takes into account tied ranks.")
+    (license license:gpl2)))
+
 (define-public r-acrm
   (package
     (name "r-acrm")
-- 
2.34.1

[bug#64250] [PATCH 11/15] gnu: Add r-cellid.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-cellid): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 00701c4463..78cab7171b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1436,6 +1436,50 @@ (define-public r-celldex
 single-cell data or deconvolution of bulk RNA-seq.")
     (license license:gpl3)))
 
+(define-public r-cellid
+  (package
+    (name "r-cellid")
+    (version "1.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "CelliD" version))
+              (sha256
+               (base32
+                "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03"))))
+    (properties `((upstream-name . "CelliD")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-data-table
+                             r-biocparallel
+                             r-fastmatch
+							 r-fgsea
+                             r-ggplot2
+                             r-glue
+                             r-irlba
+                             r-matrix
+                             r-matrixstats
+                             r-pbapply
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-reticulate
+                             r-rtsne
+                             r-seurat
+                             r-stringr
+                             r-tictoc
+							 r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-umap))
+    (native-inputs (list r-knitr r-scater))
+    (home-page "https://bioconductor.org/packages/CelliD")
+    (synopsis
+     "Single cell gene signature extraction using multiple correspondence analysis")
+    (description
+     "CelliD is a clustering-free method for extracting per-cell gene signatures from scRNA-seq.
+CelliD allows unbiased cell identity recognition across different donors,
+tissues-of-origin, model organisms and single-cell omics protocols.  The
+package can also be used to explore functional pathways enrichment in
+single cell data.")
+    (license license:gpl3)))
+
 (define-public r-champdata
   (package
     (name "r-champdata")
-- 
2.34.1

[bug#64250] [PATCH 12/15] gnu: Add r-dicekriging.

[Navid Afkhami]

* gnu/packages/cran.scm (r-dicekriging): New variable.
---
 gnu/packages/cran.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2873c3ce10..2f53c2f70d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33926,6 +33926,23 @@ (define-public r-dicedesign
 Design} (SFD) and to test their quality.")
     (license license:gpl3)))
 
+(define-public r-dicekriging
+  (package
+    (name "r-dicekriging")
+    (version "1.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "DiceKriging" version))
+              (sha256
+               (base32
+                "0jfb2li6b93fkwgjkr4jwxnvv7zb0aqk9lkf2mnv2awzh0r16pdb"))))
+    (properties `((upstream-name . "DiceKriging")))
+    (build-system r-build-system)
+    (home-page "https://dicekrigingclub.github.io/www/")
+    (synopsis "Kriging Methods for Computer Experiments")
+    (description "Estimation, validation and prediction of kriging models.")
+    (license license:gpl2+)))
+
 (define-public r-dials
   (package
     (name "r-dials")
-- 
2.34.1

[bug#64250] [PATCH 13/15] gnu: Add r-nichenetr.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-nichenetr): New variable.
---
 gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87e7c33b90..9de0470f7e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14800,6 +14800,63 @@ (define-public r-liana
 interaction inference from scRNA-seq data.")
       (license license:gpl3))))
 
+(define-public r-nichenetr
+  (let ((commit "cc3bcedfd6271df2e8ca85c8b771f7faa914cd3d")
+        (revision "1"))
+    (package
+      (name "r-nichenetr")
+      (version (git-version "1.1.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/saeyslab/nichenetr")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0jxkrk7cpwx0lbbgjrd885jxahdgk9ysfqp2drq22g486k6p2s9y"))))
+      (properties `((upstream-name . "nichenetr")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-caret
+                               r-catools
+                               r-circlize
+                               r-complexheatmap
+                               r-cowplot
+                               r-data-table
+                               r-diagrammer
+                               r-dicekriging
+                               r-dplyr
+                               r-e1071
+                               r-emoa
+                               r-fdrtool
+                               r-ggplot2
+                               r-ggpubr
+                               r-hmisc
+                               r-igraph
+                               r-limma
+                               r-magrittr
+                               r-matrix
+                               r-mlrmbo
+                               r-parallelmap
+                               r-purrr
+                               r-randomforest
+                               r-readr
+                               r-rocr
+                               r-seurat
+                               r-tibble
+                               r-tidyr))
+      (native-inputs (list r-knitr))
+	        (home-page "https://github.com/saeyslab/nichenetr")
+      (synopsis "The R implementation of the NicheNet method")
+      (description
+       "The goal of NicheNet is to study intercellular communication from a computational perspective.
+NicheNet uses human or mouse gene expression data of interacting cells
+as input and combines this with a prior model that integrates existing
+knowledge on ligand-to-target signaling paths.  This allows to predict
+ligand-receptor interactions that might drive gene expression changes
+in cells of interest.")
+      (license license:gpl3))))
+
 (define-public r-circus
   (package
     (name "r-circus")
-- 
2.34.1

[bug#64250] [PATCH 14/15] gnu: Add r-fsa.

[Navid Afkhami]

* gnu/packages/cran.scm (r-fsa): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2f53c2f70d..054c7c6f96 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11319,6 +11319,25 @@ (define-public r-dosnow
 using the @code{snow} package.")
     (license license:gpl2)))
 
+(define-public r-fsa
+  (package
+    (name "r-fsa")
+    (version "0.9.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "FSA" version))
+              (sha256
+               (base32
+                "0m63pik6bcqsbzizq8zjzilr2pxjl8b64ivdqzdnz09gmck73r5h"))))
+    (properties `((upstream-name . "FSA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-car r-dunn-test r-lmtest r-plotrix r-withr))
+    (home-page "https://fishr-core-team.github.io/FSA/")
+    (synopsis "Simple fisheries stock assessment methods")
+    (description
+     "This package provides a variety of simple fish stock assessment methods.")
+    (license license:gpl2+)))
+
 (define-public r-fstcore
   (package
     (name "r-fstcore")
-- 
2.34.1

[bug#64250] [PATCH 15/15] gnu: Add r-scriabin.

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (r-scriabin): New variable.
---
 gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9de0470f7e..ca24263c79 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9866,6 +9866,60 @@ (define-public r-sccustomize
 visualization and analysis of single-cell data using R.")
       (license license:gpl3+))))
 
+(define-public r-scriabin
+  (let ((commit "313d15e9150413e6bcad0947215da3a09c0257f5")
+        (revision "1"))
+    (package
+      (name "r-scriabin")
+      (version (git-version "0.0.0.9000" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/BlishLab/scriabin")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0k8khwcr3a281pa33h6l3wdk5igyqc4xknydiazk7qyf5w25g9zg"))))
+      (properties `((upstream-name . "scriabin")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-ade4
+                               r-cellid
+                               r-circlize
+                               r-clipr
+                               r-complexheatmap
+                               r-complexheatmap
+                               r-cowplot
+                               r-dplyr
+                               r-factoextra
+                               r-fsa
+                               r-genefilter
+                               r-ggalluvial
+                               r-ggfittext
+                               r-ggplot2
+                               r-ggsci
+                               r-limma
+                               r-magrittr
+                               r-matrix
+                               r-matrixstats
+                               r-networkd3
+                               r-nichenetr
+                               r-pbapply
+                               r-qlcmatrix
+                               r-scales
+                               r-scater
+                               r-seurat
+                               r-tibble
+                               r-tidyft
+                               r-wgcna))
+      (native-inputs (list r-knitr))
+	        (home-page "https://github.com/BlishLab/scriabin")
+      (synopsis "Single-cell resolved interaction analysis through binning")
+      (description
+       "Scriabin aims to provide a comprehensive view of cell-cell communication (CCC).
+It achieves this without requiring subsampling or aggregation.")
+      (license license:expat))))
+
 (define-public r-markdownhelpers
   (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
         (revision "1"))
-- 
2.34.1

bug#64250: [PATCH 00/15] *** R package (scriabin) ***

[Ricardo Wurmus]

My apologies for the delay.

Since r-diagrammer contains a lot of minified JavaScript without a way
for us to build it fully from source it has been moved to guix-science
(where we already had version 1.0.9).  As a consequence r-nichenetr and
r-scriabin were also moved to guix-science.

Everything else has been pushed to the Guix master branch with minor
changes to formatting and descriptions.

Thank you!

-- 
Ricardo