GNU bug report logs - #66966
[Patch] gnu: Add r-bcrank, r-bbcanalyzer, r-baynorm, r-bb, r-bayesspace, r-rcppdist, r-bayesknockdown, r-basicstarrseq, r-basics, r-basic4cseq, r-bsgenome-ecoli-ncbi-20080805, r-bags and r-breastcancervdx

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [Patch] gnu: Add r-bcrank, r-bbcanalyzer, r-baynorm, r-bb,
 r-bayesspace, r-rcppdist, r-bayesknockdown, r-basicstarrseq, r-basics,
 r-basic4cseq, r-bsgenome-ecoli-ncbi-20080805, r-bags and r-breastcancervdx
Date: Mon, 6 Nov 2023 11:59:45 +0100

* gnu/packages/bioconductor.scm (r-bcrank, r-bbcanalyzer, r-baynorm, 
r-bayesspace, r-bayesknockdown, r-basicstarrseq, r-basics, r-basic4cseq, 
r-bsgenome-ecoli-ncbi-20080805, r-bags and r-breastcancervdx): New 
variables.

* gnu/packages/cran.scm (r-bb and r-rcppdist): New variables.

Message #8 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 04/13] gnu: Add r-basic4cseq.
Date: Mon, 6 Nov 2023 12:06:40 +0100

* gnu/packages/bioconductor.scm (r-basic4cseq): New variable.

Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 40402f798f..737d1ca2de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22277,6 +22277,37 @@ (define-public r-dir-expiry
 eliminating obsolete caches generated by old versions of packages.")
     (license license:gpl3)))
 
+(define-public r-basic4cseq
+  (package
+    (name "r-basic4cseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Basic4Cseq" version))
+       (sha256
+        (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4"))))
+    (properties `((upstream-name . "Basic4Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-bsgenome-ecoli-ncbi-20080805
+           r-catools
+           r-genomicalignments
+           r-genomicranges
+           r-rcircos))
+    (home-page "https://bioconductor.org/packages/Basic4Cseq")
+    (synopsis "Analyzing 4C-seq data")
+    (description
+     "Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and
+subsequent visualization of @acronym{4C-seq, circular chromosome conformation
+capture sequencing} data.  Virtual fragment libraries can be created for any
+BSGenome package, and filter functions for both reads and fragments and basic
+quality controls are included.  Fragment data in the vicinity of the experiment's
+viewpoint can be visualized as a coverage plot based on a running median approach
+and a multi-scale contact profile.")
+    (license license:lgpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-- 
2.41.0

Message #11 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 05/13] gnu: Add r-basics.
Date: Mon, 6 Nov 2023 12:06:41 +0100

* gnu/packages/bioconductor.scm (r-basics): New variable.

Change-Id: I6f0afeeb41f667d780707af65034d5ba978f0d4a
---
 gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 737d1ca2de..184972afb5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22308,6 +22308,56 @@ (define-public r-basic4cseq
 and a multi-scale contact profile.")
     (license license:lgpl3)))
 
+(define-public r-basics
+  (package
+    (name "r-basics")
+    (version "2.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BASiCS" version))
+       (sha256
+        (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8"))))
+    (properties `((upstream-name . "BASiCS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-coda
+           r-cowplot
+           r-ggextra
+           r-ggplot2
+           r-hexbin
+           r-mass
+           r-matrix
+           r-matrixstats
+           r-posterior
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-scran
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-viridis))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/catavallejos/BASiCS")
+    (synopsis "Bayesian analysis of single-cell sequencing data")
+    (description
+     "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an
+integrated Bayesian hierarchical model to perform statistical analyses of
+single-cell RNA sequencing datasets in the context of supervised experiments
+(where the groups of cells of interest are known a priori.  BASiCS performs
+built-in data normalisation (global scaling) and technical noise quantification
+(based on spike-in genes).  BASiCS provides an intuitive detection criterion for
+highly (or lowly) variable genes within a single group of cells.  Additionally,
+BASiCS can compare gene expression patterns between two or more pre-specified
+groups of cells.")
+    (license license:gpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-- 
2.41.0

Message #14 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 07/13] gnu: Add r-bayesknockdown.
Date: Mon, 6 Nov 2023 12:06:43 +0100

* gnu/packages/bioconductor.scm (r-bayesknockdown): New variable.

Change-Id: Icceffc04071efaa8a8b79144005fa7745abc7e1a
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 986227ec38..12d9e1b077 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22441,6 +22441,30 @@ (define-public r-basilisk
 Python environments in a single R session.")
     (license license:gpl3)))
 
+(define-public r-bayesknockdown
+  (package
+    (name "r-bayesknockdown")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesKnockdown" version))
+       (sha256
+        (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8"))))
+    (properties `((upstream-name . "BayesKnockdown")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase))
+    (home-page "https://bioconductor.org/packages/BayesKnockdown")
+    (synopsis "Posterior probabilities for edges from knockdown data")
+    (description
+     "This package provides a simple, fast Bayesian method for computing posterior
+probabilities for relationships between a single predictor variable and multiple
+potential outcome variables, incorporating prior probabilities of relationships.
+In the context of knockdown experiments, the predictor variable is the
+knocked-down gene, while the other genes are potential targets.  Can also be
+used for differential expression/2-class data.")
+    (license license:gpl3)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

Message #17 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 01/13] gnu: Add r-breastcancervdx.
Date: Mon, 6 Nov 2023 12:06:37 +0100

* gnu/packages/bioconductor.scm (r-breastcancervdx): New variable.

Change-Id: Ia3437ab67a00ce23c61553ff15f940b8a3ee9c8a
---
 gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe5ca9fbc7..04a1f2a710 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1463,6 +1463,26 @@ (define-public r-breakpointrdata
 demonstrate functionalities of the @code{breakpointR} package.")
     (license license:expat)))
 
+(define-public r-breastcancervdx
+  (package
+    (name "r-breastcancervdx")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "breastCancerVDX" version
+                              'experiment))
+       (sha256
+        (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0"))))
+    (properties `((upstream-name . "breastCancerVDX")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/breastCancerVDX")
+    (synopsis "Gene expression datasets published")
+    (description
+     "This package is a collection of gene expression data from a breast cancer
+study published in Wang et al. 2005 and Minn et al 2007.")
+    (license license:artistic2.0)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")

base-commit: c9361460dece1dbc3d2645ad3e5c79e85a2bf183
-- 
2.41.0

Message #20 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 02/13] gnu: Add r-bags.
Date: Mon, 6 Nov 2023 12:06:38 +0100

* gnu/packages/bioconductor.scm (r-bags): New variable.

Change-Id: If0c533898a5e05809f23e7e8b52fc3d5fbffc8fb
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 04a1f2a710..47931061af 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4036,6 +4036,27 @@ (define-public r-baalchip
 alleles, a known phenotypical feature of cancer samples.")
     (license license:artistic2.0)))
 
+(define-public r-bags
+  (package
+    (name "r-bags")
+    (version "2.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BAGS" version))
+       (sha256
+        (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh"))))
+    (properties `((upstream-name . "BAGS")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-breastcancervdx))
+    (home-page "https://bioconductor.org/packages/BAGS")
+    (synopsis "Bayesian approach for geneset selection")
+    (description
+     "This R package is providing functions to perform geneset significance
+analysis over simple cross-sectional data between 2 and 5 phenotypes of
+interest.")
+    (license license:artistic2.0)))
+
 (define-public r-basespacer
   (package
     (name "r-basespacer")
-- 
2.41.0

Message #23 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 10/13] gnu: Add r-bb.
Date: Mon, 6 Nov 2023 12:06:46 +0100

* gnu/packages/cran.scm (r-bb): New variable.

Change-Id: Ia1f4ca93fd91d7da5c105b70683f7ecb913079a0
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 18dd82fd03..20d86487f0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6266,6 +6266,27 @@ (define-public r-rcppxptrutils
 components.")
     (license license:expat)))
 
+(define-public r-bb
+  (package
+    (name "r-bb")
+    (version "2019.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BB" version))
+       (sha256
+        (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04"))))
+    (properties `((upstream-name . "BB")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-quadprog))
+    (home-page "https://publichealth.jhu.edu/")
+    (synopsis "Solving and optimizing large-scale nonlinear systems")
+    (description
+     "This package implements Barzilai-Borwein spectral methods for solving
+nonlinear system of equations, and for optimizing nonlinear objective functions
+subject to simple constraints.")
+    (license license:gpl3)))
+
 (define-public r-bindr
   (package
     (name "r-bindr")
-- 
2.41.0

Message #26 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 11/13] gnu: Add r-baynorm.
Date: Mon, 6 Nov 2023 12:06:47 +0100

* gnu/packages/bioconductor.scm (r-baynorm): New variable.

Change-Id: I83e82d3d0362874918f423ab01f038c74f3eb265
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11ed82bc58..a8fa9d7af4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22512,6 +22512,44 @@ (define-public r-bayesspace
 features such as gene expression or cell type composition can be imputed.")
     (license license:expat)))
 
+(define-public r-baynorm
+  (package
+    (name "r-baynorm")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bayNorm" version))
+       (sha256
+        (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq"))))
+    (properties `((upstream-name . "bayNorm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bb
+           r-biocparallel
+           r-dosnow
+           r-fitdistrplus
+           r-foreach
+           r-iterators
+           r-locfit
+           r-mass
+           r-matrix
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppprogress
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/WT215/bayNorm")
+    (synopsis "Single-cell RNA sequencing data normalization")
+    (description
+     "The bayNorm package is used for normalizing single-cell RNA-seq data.  The
+main function is bayNorm, which is a wrapper function for gene specific prior
+parameter estimation and normalization.  The input is a matrix of scRNA-seq data
+with rows different genes and coloums different cells.  The output is either
+point estimates from posterior (2D array) or samples from posterior (3D array).")
+    (license license:gpl2+)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

Message #29 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 13/13] gnu: Add r-bcrank.
Date: Mon, 6 Nov 2023 12:06:49 +0100

* gnu/packages/bioconductor.scm (r-bcrank): New variable.

Change-Id: Id43ae3b7f6eff54e1180b489c90fc72176751f9f
---
 gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 384bb7cbdf..a3ce78071b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22580,6 +22580,26 @@ (define-public r-bbcanalyzer
 included in the plots.")
     (license license:lgpl3)))
 
+(define-public r-bcrank
+  (package
+    (name "r-bcrank")
+    (version "1.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BCRANK" version))
+       (sha256
+        (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9"))))
+    (properties `((upstream-name . "BCRANK")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biostrings))
+    (home-page "https://bioconductor.org/packages/BCRANK")
+    (synopsis "Predicting binding site consensus from ranked DNA sequences")
+    (description
+     "This package provides functions and classes for de novo prediction of
+transcription factor binding consensus by heuristic search.")
+    (license license:gpl2)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

Message #32 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 09/13] gnu: Add r-bayesspace.
Date: Mon, 6 Nov 2023 12:06:45 +0100

* gnu/packages/bioconductor.scm (r-bayesspace): New variable.

Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab
---
 gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 12d9e1b077..11ed82bc58 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22465,6 +22465,53 @@ (define-public r-bayesknockdown
 used for differential expression/2-class data.")
     (license license:gpl3)))
 
+(define-public r-bayesspace
+  (package
+    (name "r-bayesspace")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesSpace" version))
+       (sha256
+        (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105"))))
+    (properties `((upstream-name . "BayesSpace")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biocfilecache
+           r-biocsingular
+           r-coda
+           r-dirichletreg
+           r-ggplot2
+           r-matrix
+           r-mclust
+           r-purrr
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppdist
+           r-rcppprogress
+           r-rcurl
+           r-rhdf5
+           r-s4vectors
+           r-scales
+           r-scater
+           r-scran
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://www.ezstatconsulting.com/BayesSpace/")
+    (synopsis "Clustering and resolution enhancement of spatial transcriptomes")
+    (description
+     "This package provides tools for clustering and enhancing the resolution of
+spatial gene expression experiments.  BayesSpace clusters a low-dimensional
+representation of the gene expression matrix, incorporating a spatial prior to
+encourage neighboring spots to cluster together.  The method can enhance the
+resolution of the low-dimensional representation into \"sub-spots\", for which
+features such as gene expression or cell type composition can be imputed.")
+    (license license:expat)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

Message #35 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 03/13] gnu: Add r-bsgenome-ecoli-ncbi-20080805.
Date: Mon, 6 Nov 2023 12:06:39 +0100

* gnu/packages/bioconductor.scm (r-bsgenome-ecoli-ncbi-20080805):
    New variable.

Change-Id: Ic42527fa334be4c23ebe2e19461571d899db77ca
---
 gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 47931061af..40402f798f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -395,6 +395,28 @@ (define-public r-bsgenome-drerio-ucsc-danrer11
 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-ecoli-ncbi-20080805
+  (package
+    (name "r-bsgenome-ecoli-ncbi-20080805")
+    (version "1.3.1000")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version
+                              'annotation))
+       (sha256
+        (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27"))))
+    (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bsgenome))
+    (home-page
+     "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805")
+    (synopsis "Escherichia coli full genomes")
+    (description
+     "Escherichia coli full genomes for several strains as provided by NCBI on
+2008/08/05 and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
   (package
     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
-- 
2.41.0

Message #38 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 06/13] gnu: Add r-basicstarrseq.
Date: Mon, 6 Nov 2023 12:06:42 +0100

* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable.

Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
---
 gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 184972afb5..986227ec38 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22358,6 +22358,39 @@ (define-public r-basics
 groups of cells.")
     (license license:gpl3)))
 
+(define-public r-basicstarrseq
+  (package
+    (name "r-basicstarrseq")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BasicSTARRseq" version))
+       (sha256
+        (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa"))))
+    (properties `((upstream-name . "BasicSTARRseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BasicSTARRseq")
+    (synopsis "Basic peak calling on STARR-seq data")
+    (description
+     "This package implements a method that aims to identify enhancers on large
+scale.  The STARR-seq data consists of two sequencing datasets of the same targets
+in a specifc genome.  The input sequences show which regions where tested for
+enhancers.  Significant enriched peaks i.e. a lot more sequences in one region
+than in the input where enhancers in the genomic DNA are, can be identified.  So
+the approach pursued is to call peak every region in which there is a lot more
+(significant in a binomial model) STARR-seq signal than input signal and propose
+an enhancer at that very same position.  Enhancers then are called weak or strong
+dependent of there degree of enrichment in comparison to input.")
+    (license license:lgpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-- 
2.41.0

Message #41 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 08/13] gnu: Add r-rcppdist.
Date: Mon, 6 Nov 2023 12:06:44 +0100

* gnu/packages/cran.scm (r-rcppdist): New variable.

Change-Id: Iaa99d2b9c63f6803979ec74f471d2d60a2bf0635
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 30f28f6adc..18dd82fd03 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6132,6 +6132,30 @@ (define-public r-rcppde
 performs global optimization by differential evolution.")
     (license license:gpl2+)))
 
+(define-public r-rcppdist
+  (package
+    (name "r-rcppdist")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppDist" version))
+       (sha256
+        (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x"))))
+    (properties `((upstream-name . "RcppDist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/duckmayr/RcppDist")
+    (synopsis "Integration of additional probability distributions")
+    (description
+     "RcppDist provides a header-only C++ library with functions for additional
+statistical distributions that can be called from C++ when writing code using
+Rcpp or RcppArmadillo.  Functions are available that return a @code{NumericVector}
+as well as doubles, and for multivariate or matrix distributions, Armadillo
+vectors and matrices.")
+    (license license:gpl2+)))
+
 (define-public r-rcppml
   (package
     (name "r-rcppml")
-- 
2.41.0

Message #44 received at 66966 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Subject: [PATCH 12/13] gnu: Add r-bbcanalyzer.
Date: Mon, 6 Nov 2023 12:06:48 +0100

* gnu/packages/bioconductor.scm (r-bbcanalyzer): New variable.

Change-Id: Icd3c77c9522d73638ddb0934ad332ddb7b947a8e
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a8fa9d7af4..384bb7cbdf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22550,6 +22550,36 @@ (define-public r-baynorm
 point estimates from posterior (2D array) or samples from posterior (3D array).")
     (license license:gpl2+)))
 
+(define-public r-bbcanalyzer
+  (package
+    (name "r-bbcanalyzer")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BBCAnalyzer" version))
+       (sha256
+        (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1"))))
+    (properties `((upstream-name . "BBCAnalyzer")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-summarizedexperiment
+           r-variantannotation))
+    (home-page "https://bioconductor.org/packages/BBCAnalyzer")
+    (synopsis "Visualizing base counts")
+    (description
+     "BBCAnalyzer is a package for visualizing the relative or absolute number
+of bases, deletions and insertions at defined positions in sequence alignment
+data available as bam files in comparison to the reference bases.  Markers for
+the relative base frequencies, the mean quality of the detected bases, known
+mutations or polymorphisms and variants called in the data may additionally be
+included in the plots.")
+    (license license:lgpl3)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

Message #49 received at 66966-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 66966-done <at> debbugs.gnu.org
Subject: Re: [bug#66966] [PATCH 01/13] gnu: Add r-breastcancervdx.
Date: Mon, 13 Nov 2023 15:09:53 +0100

Hi,

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-breastcancervdx): New variable.

I just applied this patch set with minor changes to the descriptions.

Thank you!

-- 
Ricardo

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