Mădălin Ionel Patrașcu wrote 1 years ago
(address . guix-patches@gnu.org)
dcc6dea5-a444-4218-a3d7-959906aaa7f4@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-scgate, r-stacas and r-projectils):
New variables.
[PATCH] gnu: Add r-scgate, r-stacas and r-projectils.
- Done
Details
- 2 participants
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- Mădălin Ionel Patrașcu
- Severity
- normal
Mădălin Ionel Patrașcu wrote 1 years ago
[PATCH 1/3] gnu: Add r-scgate.
(address . 68056@debbugs.gnu.org)
dce9fb4afc7cc569984b722a43f51388bbb5a69f.1703671356.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-scgate): New variable.
Change-Id: Ibcf9eaef67398aa00473d29d651c6d32e425d989
---
gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
Toggle diff (56 lines)
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
Mădălin Ionel Patrașcu wrote 1 years ago
[PATCH 2/3] gnu: Add r-stacas.
(address . 68056@debbugs.gnu.org)
f8637e701714926d5ee5265758fe977dad296d0e.1703671356.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-stacas): New variable.
Change-Id: I258a315465ed88b8013d26a36718250c950aa107
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
Toggle diff (49 lines)
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
Mădălin Ionel Patrașcu wrote 1 years ago
[PATCH 3/3] gnu: Add r-projectils.
(address . 68056@debbugs.gnu.org)
94e8ffe4bb3d6ae0530bc6da99989f39a79f5f5c.1703671356.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-projectils): New variable.
Change-Id: Ia975cfcb9c79e59b029c6839dc87b5dcb89bf72a
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
Toggle diff (58 lines)
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
Ricardo Wurmus wrote 1 years ago
[PATCH] gnu: Add r-scgate, r-stacas and r-projectils.
(address . 68056-done@debbugs.gnu.org)
874jeuhjjj.fsf@elephly.net
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
Closed
Ricardo Wurmus wrote 1 years ago
(address . 68056-done@debbugs.gnu.org)
87zfwmg38h.fsf@elephly.net
Ricardo Wurmus <rekado@elephly.net> writes:
Toggle quote (5 lines)
> 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
Closed
?