[bug#60885] [PATCH 0/4] Some bioinfo packages

[bug#60885] [PATCH 0/4] Some bioinfo packages

[Simon Tournier]

Hi,

Here some pacakages used in Bioinformatics.

Note that the package numbat comes with 'bin/pileup_and_phase.R' for preparing
the data, as explained in online documentation [1].

Here, this script goes under 'site-library/numbat/bin' which does not
perfectly match the online documentation mentioning 'numbat/inst/bin/'
instead.

1: https://kharchenkolab.github.io/numbat/articles/numbat.html

Cheers,
simon

Simon Tournier (4):
  gnu: Add python-vireosnp.
  gnu: Add r-scistreer.
  gnu: Add r-roptim.
  gnu: Add r-numbat.

 gnu/packages/bioconductor.scm   | 106 +++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm |  22 +++++++
 gnu/packages/cran.scm           |  23 ++++++-
 3 files changed, 149 insertions(+), 2 deletions(-)


base-commit: ecda67a577570f412b103e5dd8ed1a44193a9c11
-- 
2.38.1

[bug#60885] [PATCH 1/4] gnu: Add python-vireosnp.

[Simon Tournier]

* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e60dffc21e..5fc2d18690 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17604,6 +17604,28 @@ (define-public r-kbet
       ;; Any version of the GPL
       (license license:gpl3+))))
 
+(define-public python-vireosnp
+  (package
+    (name "python-vireosnp")
+    (version "0.5.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "vireoSNP" version))
+              (sha256
+               (base32
+                "02ybhzivsxwnb1axlgbs63wni1j27xajnkl4jw1ps5vmsz2l4b0d"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
+    (home-page "https://github.com/huangyh09/vireoSNP")
+    (synopsis "Deconvolution based on SNP for multiplexed scRNA-seq data")
+    (description
+     "This package provides a deconvolution based on Single Nucleotide
+Position (SNP) for multiplexed scRNA-seq data.  The name vireo stand for
+Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in
+multiplexed scRNA-seq data and follows the clone identification from
+single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
+    (license license:asl2.0)))
+
 (define-public ccwl
   (package
     (name "ccwl")
-- 
2.38.1

[bug#60885] [PATCH 2/4] gnu: Add r-scistreer.

[Simon Tournier]

* gnu/packages/bioconductor.scm (r-scistreer): New variable.
---
 gnu/packages/bioconductor.scm | 39 ++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ca236bcf75..3511bfd81a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -7343,6 +7343,43 @@ (define-public r-scdblfinder
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+;; This is a CRAN package, but it depends on packages from Bioconductor.
+(define-public r-scistreer
+  (package
+    (name "r-scistreer")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "scistreer" version))
+              (sha256
+               (base32
+                "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9"))))
+    (properties `((upstream-name . "scistreer")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-dplyr
+                             r-ggplot2
+                             r-ggtree
+                             r-igraph
+                             r-paralleldist
+                             r-patchwork
+                             r-phangorn
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rcppparallel
+                             r-reshape2
+                             r-rhpcblasctl
+                             r-stringr
+                             r-tidygraph))
+    (home-page "https://github.com/kharchenkolab/scistreer")
+    (synopsis "Maximum-likelihood perfect phylogeny Inference at scale")
+    (description
+     "This packages provides fast maximum-likelihood phylogeny inference from
+noisy single-cell data using the ScisTree algorithm proposed by
+@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}.  It makes the
+method applicable to massive single-cell datasets (>10,000 cells).")
+    (license license:gpl3)))
+
 (define-public r-scmap
   (package
     (name "r-scmap")
-- 
2.38.1

[bug#60885] [PATCH 3/4] gnu: Add r-roptim.

[Simon Tournier]

* gnu/packages/cran.scm (r-roptim): New variable.
---
 gnu/packages/cran.scm | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3fcbd3b9f6..aad49b4524 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -31,7 +31,7 @@
 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
-;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
@@ -9214,6 +9214,27 @@ (define-public r-randomizr
 experimental designs and random samples for common sampling designs.")
     (license license:expat)))
 
+(define-public r-roptim
+  (package
+    (name "r-roptim")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "roptim" version))
+              (sha256
+               (base32
+                "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y"))))
+    (properties `((upstream-name . "roptim")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp r-rcpparmadillo))
+    (home-page "https://github.com/ypan1988/roptim/")
+    (synopsis "General purpose optimization in R using C++")
+    (description
+     "This package performs optimization in R using C++.  A unified wrapper
+interface is provided to call C functions of the five optimization algorithms
+('Nelder-Mead', BFGS', CG', L-BFGS-B and SANN') underlying @code{optim()}.")
+    (license license:gpl2+)))
+
 (define-public r-base64url
   (package
     (name "r-base64url")
-- 
2.38.1

[bug#60885] [PATCH 4/4] gnu: Add r-numbat.

[Simon Tournier]

* gnu/packages/bioconductor.scm (r-numbat): New variable.
---
 gnu/packages/bioconductor.scm | 67 +++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3511bfd81a..2d6093b238 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6696,6 +6696,73 @@ (define-public r-mzr
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-numbat
+  (package
+    (name "r-numbat")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "numbat" version))
+              (sha256
+               (base32
+                "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb"))))
+    (properties `((upstream-name . "numbat")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-catools
+                             r-data-table
+                             r-dendextend
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-ggraph
+                             r-ggtree
+                             r-glue
+                             r-igraph
+                             r-iranges
+                             r-logger
+                             r-magrittr
+                             r-matrix
+                             r-optparse
+                             r-paralleldist
+                             r-patchwork
+                             r-pryr
+                             r-purrr
+                             r-r-utils
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rhpcblasctl
+                             r-roptim
+                             r-scales
+                             r-scistreer
+                             r-stringr
+                             r-tibble
+                             r-tidygraph
+                             r-tidyr
+                             r-vcfr
+                             r-zoo))
+    (home-page "https://github.com/kharchenkolab/numbat")
+    (synopsis "Haplotype-aware CNV analysis from scRNA-Seq")
+    (description
+     "This package provides a computational method that infers copy number
+variations (CNV) in cancer scRNA-seq data and reconstructs the tumor
+phylogeny.  It integrates signals from gene expression, allelic ratio, and
+population haplotype structures to accurately infer allele-specific CNVs in
+single cells and reconstruct their lineage relationship.  It does not require
+tumor/normal-paired DNA or genotype data, but operates solely on the donor
+scRNA-data data (for example, 10x Cell Ranger output).  It can be used to:
+
+@enumerate
+@item detect allele-specific copy number variations from single-cells
+@item differentiate tumor versus normal cells in the tumor microenvironment
+@item infer the clonal architecture and evolutionary history of profiled tumors
+@end enumerate
+
+For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y,
+Gao et al in Nature Biotechnology 2022}.")
+    (license license:expat)))
+
 (define-public r-organism-dplyr
   (package
     (name "r-organism-dplyr")
-- 
2.38.1

bug#60885: [PATCH 0/4] Some bioinfo packages

[Ricardo Wurmus]

Thank you for the patches!  I applied them with very minor changes to
descriptions.

-- 
Ricardo