(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
7734e3c0299847c9a5c367e2bcf77a6a@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-makecdfenv, r-altcdfenvs and r-harshlight): New variables.
[PATCH] gnu: Add r-makecdfenv, r-altcdfenvs and r-harshlight.
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- M?d?lin Ionel Patra?cu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
M
M
[PATCH 2/3] gnu: Add r-altcdfenvs.
(address . 59835@debbugs.gnu.org)
20221205152153.18545-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-altcdfenvs): New variable.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
Toggle diff (44 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7cace3317c..37b84983c4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2492,6 +2492,37 @@ (define-public r-alpine
data.")
(license license:gpl2+)))
+(define-public r-altcdfenvs
+ (package
+ (name "r-altcdfenvs")
+ (version "2.60.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "altcdfenvs" version))
+ (sha256
+ (base32
+ "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0"))))
+ (properties `((upstream-name . "altcdfenvs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affy
+ r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-hypergraph
+ r-makecdfenv
+ r-s4vectors))
+ (home-page "https://bioconductor.org/packages/altcdfenvs")
+ (synopsis
+ "Convenience data structures and functions to handle CDF environments")
+ (description
+ "The package is usable with @code{Affymetrix GeneChip} short oligonucleotide
+arrays, and it can be adapted or extended to other platforms. It is able to
+modify or replace the grouping of probes in the probe sets. Also, the package
+contains simple functions to read @code{R} connections in the @code{FASTA} format
+and it can create an alternative mapping from sequences.")
+ (license license:gpl2+)))
+
(define-public r-aneufinder
(package
(name "r-aneufinder")
--
2.38.1
M
[PATCH 1/3] gnu: Add r-makecdfenv.
(address . 59835@debbugs.gnu.org)
20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-makecdfenv): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
Toggle diff (42 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c62c5970b8..7cace3317c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6010,6 +6010,33 @@ (define-public r-made4
datasets (coinertia analysis).")
(license license:artistic2.0)))
+(define-public r-makecdfenv
+ (package
+ (name "r-makecdfenv")
+ (version "1.74.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "makecdfenv" version))
+ (sha256
+ (base32
+ "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25"))))
+ (properties `((upstream-name . "makecdfenv")))
+ (build-system r-build-system)
+ (inputs (list zlib))
+ (propagated-inputs
+ (list r-affy
+ r-affyio
+ r-biobase
+ r-zlibbioc))
+ (home-page "https://bioconductor.org/packages/makecdfenv")
+ (synopsis "Chip description file environment maker")
+ (description
+ "This package implements two functions. One of them reads an @code{Affymetrix}
+@acronym{CDF, chip description file} and creates a hash table environment containing
+the location/probe set membership mapping. The other one creates a package that
+automatically loads that environment.")
+ (license license:gpl2+)))
+
(define-public r-metaneighbor
(package
(name "r-metaneighbor")
base-commit: b2a848d23d37f31496e1ff664f1dcf6abcdcc388
--
2.38.1
M
[PATCH 3/3] gnu: Add r-harshlight.
(address . 59835@debbugs.gnu.org)
20221205152153.18545-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-harshlight): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
Toggle diff (40 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 37b84983c4..346fccfd3a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5854,6 +5854,33 @@ (define-public r-gseabase
Enrichment Analysis} (GSEA).")
(license license:artistic2.0)))
+(define-public r-harshlight
+ (package
+ (name "r-harshlight")
+ (version "1.70.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Harshlight" version))
+ (sha256
+ (base32
+ "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm"))))
+ (properties `((upstream-name . "Harshlight")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-affy
+ r-altcdfenvs
+ r-biobase))
+ (home-page "http://asterion.rockefeller.edu/Harshlight/")
+ (synopsis "Corrective make-up program for microarray chips")
+ (description
+ "The package detects extended diffuse and compact blemishes on microarray
+chips. @code{Harshlight} marks the areas in a collection of chips (affybatch
+objects). A corrected @code{AffyBatch} object will result. The package replaces
+the defected areas with N/As or the median of the values of the same probe. The
+new version handles the substitute value as a whole matrix to solve the memory
+problem.")
+ (license license:gpl2+)))
+
(define-public r-hpar
(package
(name "r-hpar")
--
2.38.1
R
Re: [bug#59835] [PATCH 1/3] gnu: Add r-makecdfenv.
(name . M?d?lin Ionel Patra?cu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 59835-done@debbugs.gnu.org)
87cz8o3czj.fsf@elephly.net
I applied this series with minor changes, thanks!
--
Ricardo
Closed
?