[bug#68056] [PATCH] gnu: Add r-scgate, r-stacas and r-projectils.

[bug#68056] [PATCH] gnu: Add r-scgate, r-stacas and r-projectils.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (r-scgate, r-stacas and r-projectils): 
New variables.

[bug#68056] [PATCH 1/3] gnu: Add r-scgate.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (r-scgate): New variable.

Change-Id: Ibcf9eaef67398aa00473d29d651c6d32e425d989
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e7b99ee61..d572980965 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10301,6 +10301,47 @@ (define-public r-sccustomize
 visualization and analysis of single-cell data using R.")
       (license license:gpl3+))))
 
+(define-public r-scgate
+  (package
+    (name "r-scgate")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "scGate" version))
+       (sha256
+        (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh"))))
+    (properties `((upstream-name . "scGate")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-dplyr
+           r-ggplot2
+           r-ggridges
+           r-patchwork
+           r-reshape2
+           r-seurat
+           r-ucell))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/carmonalab/scGate")
+    (synopsis
+     "Marker-based cell type purification for single-cell sequencing data")
+    (description
+     "This package provides a method to purify a cell type or cell population of
+interest from heterogeneous datasets.  scGate package automatizes marker-based
+purification of specific cell populations, without requiring training data or
+reference gene expression profiles.  scGate takes as input a gene expression
+matrix stored in a Seurat object and a @acronym{GM, gating model}, consisting of
+a set of marker genes that define the cell population of interest.  It evaluates
+the strength of signature marker expression in each cell using the rank-based
+method UCell, and then performs @acronym{kNN, k-nearest neighbor} smoothing by
+calculating the mean UCell score across neighboring cells.  kNN-smoothing aims
+at compensating for the large degree of sparsity in scRNAseq data.  Finally, a
+universal threshold over kNN-smoothed signature scores is applied in binary
+decision trees generated from the user-provided gating model, to annotate cells
+as either “pure” or “impure”, with respect to the cell population of interest.")
+    (license license:gpl3)))
+
 (define-public r-markdownhelpers
   (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
         (revision "1"))

base-commit: 0d13d095420861022e68e87ceebd5e037e12a8b3
-- 
2.41.0

[bug#68056] [PATCH 2/3] gnu: Add r-stacas.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (r-stacas): New variable.

Change-Id: I258a315465ed88b8013d26a36718250c950aa107
---
 gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d572980965..d736abe07e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1069,6 +1069,42 @@ (define-public r-singlet
 similar.")
       (license license:gpl2+))))
 
+(define-public r-stacas
+  (package
+    (name "r-stacas")
+    (version "2.2.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/carmonalab/STACAS")
+              (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+        (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm"))))
+    (properties `((upstream-name . "STACAS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocneighbors
+           r-biocparallel
+           r-ggplot2
+           r-ggridges
+           r-pbapply
+           r-r-utils
+           r-seurat))
+    (home-page "https://github.com/carmonalab/STACAS")
+    (synopsis "Sub-type anchoring correction for alignment in Seurat")
+    (description
+      "This package implements methods for batch correction and integration of
+scRNA-seq datasets, based on the Seurat anchor-based integration framework.  In
+particular, STACAS is optimized for the integration of heterogenous datasets with
+only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with
+CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods
+would tend to over-correct biological differences.  The 2.0 version of the package
+allows the users to incorporate explicit information about cell-types in order
+to assist the integration process.")
+    (license license:gpl3)))
+
 (define-public r-stringendo
   (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a")
         (revision "1"))
-- 
2.41.0

[bug#68056] [PATCH 3/3] gnu: Add r-projectils.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (r-projectils): New variable.

Change-Id: Ia975cfcb9c79e59b029c6839dc87b5dcb89bf72a
---
 gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d736abe07e..f959de7cd6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10247,6 +10247,51 @@ (define-public r-premessa
 bead-based normalization and debarcoding.")
       (license license:gpl3))))
 
+(define-public r-projectils
+  (let ((commit "cc73b97471b4b6eea11ce779b5c4a7dc5c3e1709")
+        (revision "1"))
+    (package
+      (name "r-projectils")
+      (version (git-version "3.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/carmonalab/ProjecTILs")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0dpzvbhhb9andnj7angpj32cgkwd6rs6qgpl6i21pqzcn6vqqhqw"))))
+      (properties `((upstream-name . "ProjecTILs")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biocneighbors
+             r-biocparallel
+             r-dplyr
+             r-ggplot2
+             r-matrix
+             r-patchwork
+             r-pheatmap
+             r-pracma
+             r-purrr
+             r-rcolorbrewer
+             r-reshape2
+             r-scales
+             r-scgate
+             r-seurat
+             r-seuratobject
+             r-stacas
+             r-ucell
+             r-umap
+             r-uwot))
+      (home-page "https://github.com/carmonalab/ProjecTILs")
+      (synopsis "Reference-based analysis of scRNA-seq data")
+      (description
+       "This package implements methods to project single-cell RNA-seq data onto
+a reference atlas, enabling interpretation of unknown cell transcriptomic states
+in the the context of known, reference states.")
+      (license license:gpl3))))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
-- 
2.41.0

bug#68056: [PATCH] gnu: Add r-scgate, r-stacas and r-projectils.

[Ricardo Wurmus]

Thanks for the patches.

For r-stacas and r-scgate we already have Bioconductor packages.  Since
we also have a package for r-projectils I’m closing this issue.

-- 
Ricardo

[bug#68056] [PATCH] gnu: Add r-scgate, r-stacas and r-projectils.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> Thanks for the patches.
>
> For r-stacas and r-scgate we already have Bioconductor packages.  Since
> we also have a package for r-projectils I’m closing this issue.

Turns out that *I* actually applied them about a month ago, but I had
edited the package definitions to use bioconductor-uri instead of an
arbitrary git checkout.  Sorry for the confusion!

-- 
Ricardo