* [bug#54303] [PATCH 0/6] Some bioinfo R packages.
@ 2022-03-08 19:02 zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
2022-03-15 22:11 ` bug#54303: [PATCH 0/6] Some bioinfo R packages Ricardo Wurmus
0 siblings, 2 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:02 UTC (permalink / raw)
To: 54303; +Cc: zimoun, rekado
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
^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr.
2022-03-08 19:02 [bug#54303] [PATCH 0/6] Some bioinfo R packages zimoun
@ 2022-03-08 19:06 ` zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 2/6] gnu: Add r-polychrome zimoun
` (4 more replies)
2022-03-15 22:11 ` bug#54303: [PATCH 0/6] Some bioinfo R packages Ricardo Wurmus
1 sibling, 5 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/bioconductor.scm (r-scannotatr): New variable.
---
gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 2/6] gnu: Add r-polychrome.
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
@ 2022-03-08 19:06 ` zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 3/6] gnu: Add r-babelwhale zimoun
` (3 subsequent siblings)
4 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/cran.scm (r-polychrome): 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 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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 3/6] gnu: Add r-babelwhale.
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 2/6] gnu: Add r-polychrome zimoun
@ 2022-03-08 19:06 ` zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 4/6] gnu: Add r-carrier zimoun
` (2 subsequent siblings)
4 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/cran.scm (r-babelwhale): New variable.
---
gnu/packages/cran.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 4/6] gnu: Add r-carrier.
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 2/6] gnu: Add r-polychrome zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 3/6] gnu: Add r-babelwhale zimoun
@ 2022-03-08 19:06 ` zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 5/6] gnu: Add r-ga zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 6/6] gnu: Add r-diffcyt zimoun
4 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/cran.scm (r-carrier): 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 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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 5/6] gnu: Add r-ga.
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
` (2 preceding siblings ...)
2022-03-08 19:06 ` [bug#54303] [PATCH 4/6] gnu: Add r-carrier zimoun
@ 2022-03-08 19:06 ` zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 6/6] gnu: Add r-diffcyt zimoun
4 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/cran.scm (r-ga): New variable.
---
gnu/packages/cran.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 6/6] gnu: Add r-diffcyt.
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
` (3 preceding siblings ...)
2022-03-08 19:06 ` [bug#54303] [PATCH 5/6] gnu: Add r-ga zimoun
@ 2022-03-08 19:06 ` zimoun
4 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-08 19:06 UTC (permalink / raw)
To: 54303; +Cc: zimoun
* gnu/packages/bioconductor.scm (r-diffcyt): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
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
^ permalink raw reply related [flat|nested] 9+ messages in thread
* bug#54303: [PATCH 0/6] Some bioinfo R packages.
2022-03-08 19:02 [bug#54303] [PATCH 0/6] Some bioinfo R packages zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
@ 2022-03-15 22:11 ` Ricardo Wurmus
2022-03-15 22:37 ` [bug#54303] " zimoun
1 sibling, 1 reply; 9+ messages in thread
From: Ricardo Wurmus @ 2022-03-15 22:11 UTC (permalink / raw)
To: 54303-done
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
^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#54303] [PATCH 0/6] Some bioinfo R packages.
2022-03-15 22:11 ` bug#54303: [PATCH 0/6] Some bioinfo R packages Ricardo Wurmus
@ 2022-03-15 22:37 ` zimoun
0 siblings, 0 replies; 9+ messages in thread
From: zimoun @ 2022-03-15 22:37 UTC (permalink / raw)
To: 54303, Ricardo Wurmus, zimon toutoune; +Cc: 54303-done
Thanks!
^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2022-03-15 22:39 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2022-03-08 19:02 [bug#54303] [PATCH 0/6] Some bioinfo R packages zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 1/6] gnu: Add r-scannotatr zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 2/6] gnu: Add r-polychrome zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 3/6] gnu: Add r-babelwhale zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 4/6] gnu: Add r-carrier zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 5/6] gnu: Add r-ga zimoun
2022-03-08 19:06 ` [bug#54303] [PATCH 6/6] gnu: Add r-diffcyt zimoun
2022-03-15 22:11 ` bug#54303: [PATCH 0/6] Some bioinfo R packages Ricardo Wurmus
2022-03-15 22:37 ` [bug#54303] " zimoun
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