[bug#59835] [PATCH] gnu: Add r-makecdfenv, r-altcdfenvs and r-harshlight.

[bug#59835] [PATCH] gnu: Add r-makecdfenv, r-altcdfenvs and r-harshlight.

[MadalinIonel.Patrascu]

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* gnu/packages/bioconductor.scm (r-makecdfenv, r-altcdfenvs and r-harshlight): New variables.

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[bug#59835] [PATCH 1/3] gnu: Add r-makecdfenv.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-makecdfenv): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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

[bug#59835] [PATCH 2/3] gnu: Add r-altcdfenvs.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-altcdfenvs): New variable.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

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

[bug#59835] [PATCH 3/3] gnu: Add r-harshlight.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-harshlight): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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

bug#59835: [PATCH 1/3] gnu: Add r-makecdfenv.

[Ricardo Wurmus]

I applied this series with minor changes, thanks!

-- 
Ricardo