* [bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam.
@ 2022-10-29 23:09 MadalinIonel.Patrascu
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
0 siblings, 1 reply; 7+ messages in thread
From: MadalinIonel.Patrascu @ 2022-10-29 23:09 UTC (permalink / raw)
To: 58879
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* gnu/packages/bioconductor.scm (r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam): New variables.
Unrelated patches, added in the alphabetical order.
All the best,
Mădălin Ionel Patrașcu!
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^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#58879] [PATCH 1/5] gnu: Add r-deco.
2022-10-29 23:09 [bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam MadalinIonel.Patrascu
@ 2022-10-29 23:16 ` Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease Mădălin Ionel Patrașcu
` (4 more replies)
0 siblings, 5 replies; 7+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-29 23:16 UTC (permalink / raw)
To: 58879; +Cc: rekado
* gnu/packages/bioconductor.scm (r-deco): New variable.
---
gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..2f2268e5e6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3075,6 +3075,48 @@ (define-public r-decipher
biological sequences.")
(license license:gpl3)))
+(define-public r-deco
+ (package
+ (name "r-deco")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "deco" version))
+ (sha256
+ (base32
+ "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m"))))
+ (properties `((upstream-name . "deco")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ade4
+ r-annotationdbi
+ r-biobase
+ r-biocparallel
+ r-biocstyle
+ r-cluster
+ r-foreign
+ r-gdata
+ r-ggplot2
+ r-gplots
+ r-gridextra
+ r-limma
+ r-locfit
+ r-made4
+ r-rcolorbrewer
+ r-reshape2
+ r-scatterplot3d
+ r-sfsmisc
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/fjcamlab/deco")
+ (synopsis "Decomposing heterogeneous cohorts using omic data profiling")
+ (description
+ "The package discovers differential features in hetero- and homogeneous omic
+data by a two-step method including subsampling @code{LIMMA} and @code{NSCA}.
+@code{DECO} reveals feature associations to hidden subclasses not exclusively
+related to higher deregulation levels.")
+ (license (license:fsdg-compatible "GPL (>=3)"))))
+
(define-public r-deconvr
(package
(name "r-deconvr")
base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260
--
2.38.0
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease.
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
@ 2022-10-29 23:16 ` Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig Mădălin Ionel Patrașcu
` (3 subsequent siblings)
4 siblings, 0 replies; 7+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-29 23:16 UTC (permalink / raw)
To: 58879; +Cc: rekado
* gnu/packages/bioconductor.scm (r-decomplexdisease): New variable.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f2268e5e6..809ba69bc3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3117,6 +3117,39 @@ (define-public r-deco
related to higher deregulation levels.")
(license (license:fsdg-compatible "GPL (>=3)"))))
+(define-public r-decomplexdisease
+ (package
+ (name "r-decomplexdisease")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEComplexDisease" version))
+ (sha256
+ (base32
+ "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d"))))
+ (properties `((upstream-name . "DEComplexDisease")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocparallel
+ r-complexheatmap
+ r-deseq2
+ r-edger
+ r-rcpp
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/DEComplexDisease")
+ (synopsis "Investigations of complex diseases by bi-clustering analysis")
+ (description
+ "@code{DEComplexDisease} is designed to find the @acronym{DEGs, Differential
+Expressed Genes} for complex disease, which is characterized by the heterogeneous
+genomic expression profiles. Different from the established DEG analysis tools,
+it does not assume the patients of complex diseases to share the common DEGs.
+By applying a bi-clustering algorithm, @code{DEComplexDisease} finds the DEGs
+shared by as many patients. Applying the @code{DEComplexDisease} analysis
+results, users are possible to find the patients affected by the same mechanism
+based on the shared signatures.")
+ (license license:gpl3)))
+
(define-public r-deconvr
(package
(name "r-deconvr")
--
2.38.0
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig.
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease Mădălin Ionel Patrașcu
@ 2022-10-29 23:16 ` Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq Mădălin Ionel Patrașcu
` (2 subsequent siblings)
4 siblings, 0 replies; 7+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-29 23:16 UTC (permalink / raw)
To: 58879; +Cc: rekado
* gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 809ba69bc3..7f6ba37bf8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3150,6 +3150,49 @@ (define-public r-decomplexdisease
based on the shared signatures.")
(license license:gpl3)))
+(define-public r-decomptumor2sig
+ (package
+ (name "r-decomptumor2sig")
+ (version "2.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "decompTumor2Sig" version))
+ (sha256
+ (base32
+ "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6"))))
+ (properties `((upstream-name . "decompTumor2Sig")))
+ (build-system r-build-system)
+ (inputs (list perl)) ;script/extractSpecColumns.pl
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biostrings
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-data-table
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-ggseqlogo
+ r-gridextra
+ r-matrix
+ r-plyr
+ r-quadprog
+ r-readxl
+ r-s4vectors
+ r-summarizedexperiment
+ r-txdb-hsapiens-ucsc-hg19-knowngene
+ r-variantannotation))
+ (native-inputs (list r-knitr))
+ (home-page "https://rmpiro.net/decompTumor2Sig/")
+ (synopsis "Decomposition of individual tumors into mutational signatures")
+ (description
+ "The package uses quadratic programming for signature refitting, i.e., to
+decompose the mutation catalog from an individual tumor sample into a set of given
+mutational signatures (either Alexandrov-model signatures or Shiraishi-model
+signatures), computing weights that reflect the contributions of the signatures
+to the mutation load of the tumor.")
+ (license license:gpl2)))
+
(define-public r-deconvr
(package
(name "r-deconvr")
--
2.38.0
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq.
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig Mădălin Ionel Patrașcu
@ 2022-10-29 23:16 ` Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 5/5] gnu: Add r-decontam Mădălin Ionel Patrașcu
2022-10-31 19:06 ` bug#58879: [PATCH 1/5] gnu: Add r-deco Ricardo Wurmus
4 siblings, 0 replies; 7+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-29 23:16 UTC (permalink / raw)
To: 58879; +Cc: rekado
* gnu/packages/bioconductor.scm (r-deconrnaseq): 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 7f6ba37bf8..ce95a9e5af 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3193,6 +3193,33 @@ (define-public r-decomptumor2sig
to the mutation load of the tumor.")
(license license:gpl2)))
+(define-public r-deconrnaseq
+ (package
+ (name "r-deconrnaseq")
+ (version "1.38.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DeconRNASeq" version))
+ (sha256
+ (base32
+ "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6"))))
+ (properties `((upstream-name . "DeconRNASeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ggplot2
+ r-limsolve
+ r-pcamethods))
+ (home-page "https://bioconductor.org/packages/DeconRNASeq")
+ (synopsis
+ "Deconvolution of heterogeneous tissue samples for mRNA-Seq data")
+ (description
+ "@code{DeconSeq} is an R package for deconvolution of heterogeneous tissues
+based on mRNA-Seq data. It models the expression levels from heterogeneous cell
+populations in mRNA-Seq as the weighted average of expression from different
+constituting cell types and predicted cell type proportions of single expression
+profiles.")
+ (license license:gpl2)))
+
(define-public r-deconvr
(package
(name "r-deconvr")
--
2.38.0
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#58879] [PATCH 5/5] gnu: Add r-decontam.
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
` (2 preceding siblings ...)
2022-10-29 23:16 ` [bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq Mădălin Ionel Patrașcu
@ 2022-10-29 23:16 ` Mădălin Ionel Patrașcu
2022-10-31 19:06 ` bug#58879: [PATCH 1/5] gnu: Add r-deco Ricardo Wurmus
4 siblings, 0 replies; 7+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-10-29 23:16 UTC (permalink / raw)
To: 58879; +Cc: rekado
* gnu/packages/bioconductor.scm (r-decontam): 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 ce95a9e5af..e1175e46f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3220,6 +3220,33 @@ (define-public r-deconrnaseq
profiles.")
(license license:gpl2)))
+(define-public r-decontam
+ (package
+ (name "r-decontam")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "decontam" version))
+ (sha256
+ (base32
+ "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9"))))
+ (properties `((upstream-name . "decontam")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ggplot2
+ r-reshape2))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/benjjneb/decontam")
+ (synopsis
+ "Identification of the contaminants in marker-gene and metagenomics data")
+ (description
+ "This package offers simple statistical identification of contaminating
+sequence features in marker-gene or metagenomics data. Works on any kind of
+feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic
+groups, MAGs,...). Requires DNA quantitation data or sequenced negative control
+samples.")
+ (license license:artistic2.0)))
+
(define-public r-deconvr
(package
(name "r-deconvr")
--
2.38.0
^ permalink raw reply related [flat|nested] 7+ messages in thread
* bug#58879: [PATCH 1/5] gnu: Add r-deco.
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
` (3 preceding siblings ...)
2022-10-29 23:16 ` [bug#58879] [PATCH 5/5] gnu: Add r-decontam Mădălin Ionel Patrașcu
@ 2022-10-31 19:06 ` Ricardo Wurmus
4 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2022-10-31 19:06 UTC (permalink / raw)
To: Mădălin Ionel Patrașcu; +Cc: 58879-done
Applied all with minor changes (indentation, license, description).
Thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread
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2022-10-29 23:09 [bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam MadalinIonel.Patrascu
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 5/5] gnu: Add r-decontam Mădălin Ionel Patrașcu
2022-10-31 19:06 ` bug#58879: [PATCH 1/5] gnu: Add r-deco Ricardo Wurmus
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