GNU bug report logs - #66921
[patch] Add r-screpertoire, r-powertcr, r-evmix, r-truncdist and r-evd

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [patch] Add r-screpertoire, r-powertcr, r-evmix, r-truncdist and r-evd
Date: Fri, 3 Nov 2023 17:27:12 +0100

* gnu/packages/bioconductor.scm (r-screpertoire and r-powertcr): New 
variables.

* gnu/packages/cran.scm (r-evmix, r-truncdist and r-evd): New variable.

Message #8 received at 66921 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66921 <at> debbugs.gnu.org>
Subject: [PATCH 1/5] gnu: Add r-evd.
Date: Fri, 3 Nov 2023 17:30:00 +0100

* gnu/packages/cran.scm (r-evd): New variable.

Change-Id: I1f3b2ee5829807f6f76cf87b4df43ae8005688bc
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f2a035555b..b8ae1fad14 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7112,6 +7112,28 @@ (define-public r-etrunct
 which should be seen for details.")
    (license license:expat)))
 
+(define-public r-evd
+  (package
+    (name "r-evd")
+    (version "2.3-6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "evd" version))
+       (sha256
+        (base32 "0wc95hfj0gwkyghipdrhwd3s6q2agh9x2wy6y7dr6mjw7wnmjb36"))))
+    (properties `((upstream-name . "evd")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=evd")
+    (synopsis "Functions for extreme value distributions")
+    (description
+     "This package extends simulation, distribution, quantile and density
+functions to univariate and multivariate parametric extreme value distributions,
+and provides fitting functions which calculate maximum likelihood estimates for
+univariate and bivariate maxima models, and for univariate and bivariate
+threshold models.")
+    (license license:gpl3)))
+
 (define-public r-excelr
   (package
     (name "r-excelr")

base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d
-- 
2.41.0

Message #11 received at 66921 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66921 <at> debbugs.gnu.org>
Subject: [PATCH 2/5] gnu: Add r-truncdist.
Date: Fri, 3 Nov 2023 17:30:01 +0100

* gnu/packages/cran.scm (r-truncdist): New variable.

Change-Id: Icb9f06a36e5ee5a58828dc2f496b71a850a911b9
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b8ae1fad14..d7334963ec 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8856,6 +8856,30 @@ (define-public r-truncnorm
 functions, as well as a random generation function.")
     (license license:gpl2)))
 
+(define-public r-truncdist
+  (package
+    (name "r-truncdist")
+    (version "1.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "truncdist" version))
+       (sha256
+        (base32 "02ihw4ixhadwr3sqm6r264i8vpcaz8pn69vkzabd8fwqvn5vcj5q"))))
+    (properties `((upstream-name . "truncdist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-evd))
+    (home-page "https://cran.r-project.org/package=truncdist")
+    (synopsis "Truncated random variables")
+    (description
+     "This package provides a collection of tools to evaluate probability density
+functions, cumulative distribution functions, quantile functions and random
+numbers for truncated random variables.  These functions are provided to also
+compute the expected value and variance.  @acronym{Q-Q, quantile–quantile} plots
+can be produced.  All the probability functions in the stats, stats4 and evd
+packages are automatically available for truncation.")
+    (license license:gpl2+)))
+
 (define-public r-rsolnp
   (package
     (name "r-rsolnp")
-- 
2.41.0

Message #14 received at 66921 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66921 <at> debbugs.gnu.org>
Subject: [PATCH 4/5] gnu: Add r-powertcr.
Date: Fri, 3 Nov 2023 17:30:03 +0100

* gnu/packages/bioconductor.scm (r-powertcr): New variable.

Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d79236ea26..b683868df5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9236,6 +9236,37 @@ (define-public r-piano
 set analyses.")
     (license license:gpl2+)))
 
+(define-public r-powertcr
+  (package
+    (name "r-powertcr")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "powerTCR" version))
+       (sha256
+        (base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i"))))
+    (properties `((upstream-name . "powerTCR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cubature
+           r-doparallel
+           r-evmix
+           r-foreach
+           r-magrittr
+           r-purrr
+           r-truncdist
+           r-vegan
+           r-vgam))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/powerTCR")
+    (synopsis "Model-based comparative analysis of the TCR repertoire")
+    (description
+     "This package provides a model for the clone size distribution of the
+@acronym{TCR, T-cell receptor} repertoire.  Further, it permits comparative
+analysis of TCR repertoire libraries based on theoretical model fits.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package:
 ;; r-aroma-light, r-dnacopy..
 (define-public r-pscbs
-- 
2.41.0

Message #17 received at 66921 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66921 <at> debbugs.gnu.org>
Subject: [PATCH 5/5] gnu: Add r-screpertoire.
Date: Fri, 3 Nov 2023 17:30:04 +0100

* gnu/packages/bioconductor.scm (r-screpertoire): New variable.

Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
---
 gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b683868df5..8306b703de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10014,6 +10014,49 @@ (define-public r-scmap
 different experiment.")
     (license license:gpl3)))
 
+(define-public r-screpertoire
+  (package
+    (name "r-screpertoire")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scRepertoire" version))
+       (sha256
+        (base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1"))))
+    (properties `((upstream-name . "scRepertoire")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-doparallel
+           r-dplyr
+           r-ggalluvial
+           r-ggplot2
+           r-ggraph
+           r-igraph
+           r-plyr
+           r-powertcr
+           r-reshape2
+           r-rlang
+           r-seuratobject
+           r-singlecellexperiment
+           r-stringdist
+           r-stringr
+           r-summarizedexperiment
+           r-tidygraph
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scRepertoire")
+    (synopsis "Toolkit for single-cell immune receptor profiling")
+    (description
+     "The scRepertoire package was built to process data derived from the 10x
+Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and
+@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with
+the popular Seurat and SingleCellExperiment R packages.  It also allows for
+general analysis of single-cell clonotype information without the use of
+expression information.  The package functions as a wrapper for Startrac and
+powerTCR R packages.")
+    (license license:gpl2)))
+
 (define-public r-scry
   (package
     (name "r-scry")
-- 
2.41.0

Message #20 received at 66921 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66921 <at> debbugs.gnu.org>
Subject: [PATCH 3/5] gnu: Add r-evmix.
Date: Fri, 3 Nov 2023 17:30:02 +0100

* gnu/packages/cran.scm (r-evmix): New variable.

Change-Id: I93152dee218e9cef85dd66e17231f1728f0ffb52
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d7334963ec..bc3158eea6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7134,6 +7134,35 @@ (define-public r-evd
 threshold models.")
     (license license:gpl3)))
 
+(define-public r-evmix
+  (package
+    (name "r-evmix")
+    (version "2.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "evmix" version))
+       (sha256
+        (base32 "02rabc9snci00s1x7h0svfr66lmw1wjcdg0149wc52mnccsdaivf"))))
+    (properties `((upstream-name . "evmix")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gsl
+           r-mass
+           r-sparsem))
+    (home-page "http://www.math.canterbury.ac.nz/~c.scarrott/evmix.shtml")
+    (synopsis
+     "Extreme value threshold estimation and uncertainty quantification")
+    (description
+     "This package provides the usual distribution functions, maximum likelihood
+inference and model diagnostics for univariate stationary extreme value mixture
+models.  Also, there are provided kernel density estimation including various
+boundary corrected kernel density estimation methods and a wide choice of kernels,
+with cross-validation likelihood based bandwidth estimator.  Reasonable
+consistency with the base functions in the evd package is provided, so that users
+can safely interchange most code.")
+    (license license:gpl3)))
+
 (define-public r-excelr
   (package
     (name "r-excelr")
-- 
2.41.0

Message #25 received at 66921-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 66921-done <at> debbugs.gnu.org
Subject: Re: [bug#66921] [PATCH 1/5] gnu: Add r-evd.
Date: Sat, 04 Nov 2023 23:14:12 +0100

Thanks for the patches.  I’ve applied the series.

-- 
Ricardo

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