[PATCH 0/6] Some bioinfo R packages.

DoneSubmitted by zimoun.
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2 participants
  • Ricardo Wurmus
  • zimoun
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unassigned
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normal
Z
Z
zimoun wrote on 8 Mar 20:02 +0100
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190250.1010303-1-zimon.toutoune@gmail.com
Hi,

Various packages.

zimoun (6):
gnu: Add r-scannotatr.
gnu: Add r-polychrome.
gnu: Add r-babelwhale.
gnu: Add r-carrier.
gnu: Add r-ga.
gnu: Add r-diffcyt.

gnu/packages/bioconductor.scm | 75 ++++++++++++++++++++++++
gnu/packages/cran.scm | 107 ++++++++++++++++++++++++++++++++++
2 files changed, 182 insertions(+)


base-commit: 0d14f8a8702ec8016ac58e5778a754b3105ef418
--
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 1/6] gnu: Add r-scannotatr.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-1-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-scannotatr): New variable.
---
gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)

Toggle diff (50 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 534204a16a..8fcd43f27f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4349,6 +4349,43 @@ (define-public r-samr
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
+(define-public r-scannotatr
+  (package
+    (name "r-scannotatr")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "scAnnotatR" version))
+        (sha256
+          (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21"))))
+    (properties `((upstream-name . "scAnnotatR")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-annotationhub
+            r-ape
+            r-caret
+            r-data-tree
+            r-dplyr
+            r-e1071
+            r-ggplot2
+            r-kernlab
+            r-proc
+            r-rocr
+            r-seurat
+            r-singlecellexperiment
+            r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/grisslab/scAnnotatR")
+    (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
+    (description
+      "This package comprises a set of pretrained machine learning models to
+predict basic immune cell types.  This enables to quickly get a first
+annotation of the cell types present in the dataset without requiring prior
+knowledge.  The package also allows to train using own models to predict new
+cell types based on specific research needs.")
+    (license license:expat)))
+
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
-- 
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 2/6] gnu: Add r-polychrome.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-2-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-polychrome): New variable.
---
gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4178971251..488a5c5bd4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1097,6 +1097,31 @@ (define-public r-plotfunctions
 with default R plot functions.")
     (license license:gpl2+)))
 
+(define-public r-polychrome
+  (package
+    (name "r-polychrome")
+    (version "1.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "Polychrome" version))
+        (sha256
+          (base32 "044vbylgbqf0ccv4r15nmbw1vz0j95g67i6blw73hvbvbm6w5x4d"))))
+    (properties `((upstream-name . "Polychrome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-colorspace r-scatterplot3d))
+    (native-inputs
+     (list r-knitr))
+    (home-page "http://oompa.r-forge.r-project.org/")
+    (synopsis "Qualitative palettes with many colors")
+    (description
+      "This package provides tools for creating, viewing, and assessing
+qualitative palettes with many (20-30 or more) colors.  See Coombes and
+colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
+    (license license:asl2.0)))
+
+
 (define-public r-ecp
   (package
     (name "r-ecp")
-- 
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 3/6] gnu: Add r-babelwhale.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-3-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-babelwhale): New variable.
---
gnu/packages/cran.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)

Toggle diff (35 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 488a5c5bd4..46f0fb380f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -436,6 +436,28 @@ (define-public r-rticles
 for authoring journal articles and conference submissions.")
     (license license:gpl3)))
 
+(define-public r-babelwhale
+  (package
+    (name "r-babelwhale")
+    (version "1.0.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "babelwhale" version))
+        (sha256
+          (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
+    (properties `((upstream-name . "babelwhale")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
+    (home-page "https://github.com/dynverse/babelwhale")
+    (synopsis "Talking to Docker and Singularity containers")
+    (description
+      "This package provides a unified interface to interact with Docker and
+Singularity containers.  You can execute a command inside a container, mount a
+volume or copy a file.")
+    (license license:expat)))
+
 (define-public r-benchmarkmedata
   (package
     (name "r-benchmarkmedata")
-- 
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 4/6] gnu: Add r-carrier.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-4-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-carrier): New variable.
---
gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)

Toggle diff (37 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 46f0fb380f..cd19de60b3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -614,6 +614,30 @@ (define-public r-dot
 programming packages such as @code{knitr} and @code{rmarkdown}.")
     (license license:expat)))
 
+(define-public r-carrier
+  (package
+    (name "r-carrier")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "carrier" version))
+        (sha256
+          (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
+    (properties `((upstream-name . "carrier")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-pryr r-rlang))
+    (home-page "https://github.com/r-lib/carrier")
+    (synopsis "Isolate functions for remote execution")
+    (description
+      "Sending functions to remote processes can be wasteful of resources
+because they carry their environments with them.  With this package, it is
+easy to create functions that are isolated from their environment.  These
+isolated functions, also called crates, print at the console with their total
+size and can be easily tested locally before being sent to a remote.")
+    (license license:gpl3)))
+
 (define-public r-clipr
   (package
     (name "r-clipr")
-- 
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 5/6] gnu: Add r-ga.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-5-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-ga): New variable.
---
gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)

Toggle diff (49 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cd19de60b3..1fd57fb22c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1216,6 +1216,42 @@ (define-public r-ellipsis
 are not used.")
     (license license:gpl3)))
 
+(define-public r-ga
+  (package
+    (name "r-ga")
+    (version "3.2.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "GA" version))
+        (sha256
+          (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
+    (properties `((upstream-name . "GA")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-cli
+            r-crayon
+            r-foreach
+            r-iterators
+            r-rcpp
+            r-rcpparmadillo))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://luca-scr.github.io/GA/")
+    (synopsis "Genetic algorithms for stochastic optimisation")
+    (description
+      "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
+for stochastic optimisation.  Binary, real-valued, and permutation
+representations are available to optimize a fitness function, i.e., a function
+provided by users depending on their objective function.  Several genetic
+operators are available and can be combined to explore the best settings for
+the current task.  Furthermore, users can define new genetic operators and
+easily evaluate their performances.  Local search using general-purpose
+optimisation algorithms can be applied stochastically to exploit interesting
+regions.  GAs can be run sequentially or in parallel, using an explicit
+master-slave parallelisation or a coarse-grain islands approach.")
+    (license license:gpl2+)))
+
 (define-public r-grr
   (package
     (name "r-grr")
-- 
2.34.0
Z
Z
zimoun wrote on 8 Mar 20:06 +0100
[PATCH 6/6] gnu: Add r-diffcyt.
(address . 54303@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220308190617.1011563-6-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-diffcyt): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)

Toggle diff (51 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8fcd43f27f..6c5de0542c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2966,6 +2966,44 @@ (define-public r-dexseq
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-diffcyt
+  (package
+    (name "r-diffcyt")
+    (version "1.14.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "diffcyt" version))
+        (sha256
+          (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni"))))
+    (properties `((upstream-name . "diffcyt")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-circlize
+            r-complexheatmap
+            r-dplyr
+            r-edger
+            r-flowcore
+            r-flowsom
+            r-limma
+            r-lme4
+            r-magrittr
+            r-multcomp
+            r-reshape2
+            r-s4vectors
+            r-summarizedexperiment
+            r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/lmweber/diffcyt")
+    (synopsis "Differential discovery in high-dimensional cytometry")
+    (description
+      "Statistical methods for differential discovery analyses in
+high-dimensional cytometry data (including flow cytometry, mass cytometry or
+CyTOF, and oligonucleotide-tagged cytometry), based on a combination of
+high-resolution clustering and empirical Bayes moderated tests adapted from
+transcriptomics.")
+    (license license:expat)))
+
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-- 
2.34.0
R
R
Ricardo Wurmus wrote on 15 Mar 23:11 +0100
[PATCH 0/6] Some bioinfo R packages.
(address . 54303-done@debbugs.gnu.org)
87ee32n9u7.fsf@elephly.net
Thanks for the patches!

I changed indentation and some descriptions (because “guix import”
doesn’t make things look quite right) and pushed your patches on top of
a whole bunch of CRAN upgrades.

--
Ricardo
Closed
Z
Z
zimoun wrote on 15 Mar 23:37 +0100
(address . 54303-done@debbugs.gnu.org)
CAJ3okZ0e9_fff1goDFrFBzLOjJmD0yjxdwQKfh1HqFAmFp+pJg@mail.gmail.com
Thanks!
?
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