From: zimoun <zimon.toutoune@gmail.com>
To: 47171@debbugs.gnu.org
Cc: rekado@elephly.net, zimoun <zimon.toutoune@gmail.com>
Subject: [bug#47171] [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor).
Date: Wed, 17 Mar 2021 21:14:12 +0100 [thread overview]
Message-ID: <20210317201414.10811-1-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210315180714.8233-1-zimon.toutoune@gmail.com>
* gnu/packages/cran.scm (r-bisquerna): Move this variable from here...
* gnu/packages/bioconductor.scm (r-bisquerna): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/cran.scm | 25 -------------------------
2 files changed, 26 insertions(+), 25 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d611f3a491..b5ac2750f3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1294,6 +1294,32 @@ naming and share the same rich and consistent \"Vector API\" as much as
possible.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
+(define-public r-bisquerna
+ (package
+ (name "r-bisquerna")
+ (version "1.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "BisqueRNA" version))
+ (sha256
+ (base32
+ "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+ (properties `((upstream-name . "BisqueRNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-limsolve" ,r-limsolve)))
+ (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
+ (synopsis "Decomposition of bulk expression with single-cell sequencing")
+ (description "This package provides tools to accurately estimate cell type
+abundances from heterogeneous bulk expression. A reference-based method
+utilizes single-cell information to generate a signature matrix and
+transformation of bulk expression for accurate regression based estimates.
+A marker-based method utilizes known cell-specific marker genes to measure
+relative abundances across samples.")
+ (license license:gpl3)))
+
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5617383cbc..93fe44c25c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2838,31 +2838,6 @@ where the bound function accepts additional arguments.")
bindings that call a C++ function.")
(license license:expat)))
-(define-public r-bisquerna
- (package
- (name "r-bisquerna")
- (version "1.0.4")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "BisqueRNA" version))
- (sha256
- (base32
- "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
- (properties `((upstream-name . "BisqueRNA")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-limsolve" ,r-limsolve)))
- (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
- (synopsis "Decomposition of bulk expression with single-cell sequencing")
- (description "This package provides tools to accurately estimate cell type
-abundances from heterogeneous bulk expression. A reference-based method
-utilizes single-cell information to generate a signature matrix and
-transformation of bulk expression for accurate regression based estimates.
-A marker-based method utilizes known cell-specific marker genes to measure
-relative abundances across samples.")
- (license license:gpl3)))
-
(define-public r-auc
(package
(name "r-auc")
base-commit: d79d63e7829d53f6a501d8df7e264ff70033abca
--
2.30.1
next prev parent reply other threads:[~2021-03-17 20:15 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-15 18:07 [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 01/10] gnu: r-limma: Move " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 02/10] gnu: r-xvector: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 03/10] gnu: r-genomicranges: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 04/10] gnu: r-biobase: " zimoun
2021-03-15 18:08 ` [bug#47171] [PATCH 05/10] gnu: r-annotationdbi: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 06/10] gnu: r-biomart: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 07/10] gnu: r-biocparallel: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 08/10] gnu: r-biostrings: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 09/10] gnu: r-rsamtools: " zimoun
2021-03-15 18:09 ` [bug#47171] [PATCH 10/10] gnu: r-delayedarray: " zimoun
2021-03-15 22:33 ` bug#47171: [PATCH 00/10] Move some Bioconductor packages " Ricardo Wurmus
2021-03-15 23:56 ` [bug#47171] " Leo Famulari
2021-03-16 12:27 ` zimoun
2021-03-16 13:20 ` Ricardo Wurmus
2021-03-16 13:30 ` zimoun
2021-03-16 16:08 ` Ricardo Wurmus
2021-03-16 16:36 ` zimoun
2021-03-16 22:04 ` Ricardo Wurmus
2021-03-17 20:15 ` zimoun
2021-03-17 20:14 ` zimoun [this message]
2021-03-17 20:14 ` [bug#47171] [PATCH v2 2/3] gnu: r-absfiltergsea: Move " zimoun
2021-03-17 20:14 ` [bug#47171] [PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail." zimoun
2021-03-31 19:29 ` bug#47171: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor) Ricardo Wurmus
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