* [bug#56098] gnu: Add r-microbiome, r-ancombc.
@ 2022-06-19 20:39 MadalinIonel.Patrascu
2022-06-19 20:42 ` [bug#56098] [PATCH 1/2] gnu: Add r-microbiome Mădălin Ionel Patrașcu
2022-11-24 17:06 ` bug#56098: gnu: Add r-microbiome, r-ancombc Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: MadalinIonel.Patrascu @ 2022-06-19 20:39 UTC (permalink / raw)
To: 56098
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^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#56098] [PATCH 1/2] gnu: Add r-microbiome.
2022-06-19 20:39 [bug#56098] gnu: Add r-microbiome, r-ancombc MadalinIonel.Patrascu
@ 2022-06-19 20:42 ` Mădălin Ionel Patrașcu
2022-06-19 20:42 ` [bug#56098] [PATCH 2/2] gnu: Add r-ancombc Mădălin Ionel Patrașcu
2022-11-24 17:06 ` bug#56098: gnu: Add r-microbiome, r-ancombc Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-06-19 20:42 UTC (permalink / raw)
To: 56098
* gnu/packages/bioconductor.scm (r-microbiome): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..54280a26f6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8100,6 +8100,44 @@ (define-public r-bumphunter
studies.")
(license license:artistic2.0)))
+(define-public r-microbiome
+ (package
+ (name "r-microbiome")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "microbiome" version))
+ (sha256
+ (base32
+ "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12"))))
+ (properties `((upstream-name . "microbiome")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biostrings
+ r-compositions
+ r-dplyr
+ r-ggplot2
+ r-phyloseq
+ r-reshape2
+ r-rtsne
+ r-scales
+ r-tibble
+ r-tidyr
+ r-vegan))
+ (native-inputs (list r-knitr))
+ (home-page "https://microbiome.github.io/microbiome/")
+ (synopsis "Tools for microbiome analysis")
+ (description
+ "The @code{microbiome} facilitates @code{phyloseq} exploration and analysis
+of taxonomic profiling data. This package provides tools for the manipulation,
+statistical analysis, and visualization of taxonomic profiling data. In addition
+to targeted case-control studies, the @code{microbiome} facilitates scalable
+exploration of population cohorts. This package supports the independent
+@code{phyloseq} data format and expands the available toolkit in order to
+facilitate the standardization of the analyses and the development of best
+practices.")
+ (license license:bsd-2)))
+
(define-public r-minfi
(package
(name "r-minfi")
base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21
--
2.36.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#56098] [PATCH 2/2] gnu: Add r-ancombc.
2022-06-19 20:42 ` [bug#56098] [PATCH 1/2] gnu: Add r-microbiome Mădălin Ionel Patrașcu
@ 2022-06-19 20:42 ` Mădălin Ionel Patrașcu
0 siblings, 0 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-06-19 20:42 UTC (permalink / raw)
To: 56098
* gnu/packages/bioconductor.scm (r-ancombc): New variable.
---
gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 54280a26f6..a9b19bfadd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,52 @@ (define-public r-agimicrorna
objects are used so that other packages could be used as well.")
(license license:gpl3)))
+(define-public r-ancombc
+ (package
+ (name "r-ancombc")
+ (version "1.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ANCOMBC" version))
+ (sha256
+ (base32
+ "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq"))))
+ (properties `((upstream-name . "ANCOMBC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-desctools
+ r-doparallel
+ r-dorng
+ r-dplyr
+ r-energy
+ r-foreach
+ r-hmisc
+ r-magrittr
+ r-mass
+ r-microbiome
+ r-nlme
+ r-nloptr
+ r-phyloseq
+ r-rdpack
+ r-rlang
+ r-tibble
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/FrederickHuangLin/ANCOMBC")
+ (synopsis "Analysis of compositions of microbiomes with bias correction")
+ (description
+ "@code{ANCOMBC} is a package containing @dfn{DA} (differential abundance)
+and correlation analyses for microbiome data. Specifically, the package includes
+@dfn{ANCOM-BC} (Analysis of Compositions of Microbiomes with Bias Correction) and
+@dfn{ANCOM} (Analysis of Composition of Microbiomes) for DA analysis, and
+@dfn{SECOM} (Sparse Estimation of Correlations among Microbiomes) for correlation
+analysis. Microbiome data are typically subject to two sources of biases:
+unequal sampling fractions (sample-specific biases) and differential sequencing
+efficiencies (taxon-specific biases). Methodologies included in the @code{ANCOMBC}
+package were designed to correct these biases and construct statistically
+consistent estimators.")
+ (license license:artistic2.0)))
+
(define-public r-aneufinder
(package
(name "r-aneufinder")
--
2.36.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#56098: gnu: Add r-microbiome, r-ancombc.
2022-06-19 20:39 [bug#56098] gnu: Add r-microbiome, r-ancombc MadalinIonel.Patrascu
2022-06-19 20:42 ` [bug#56098] [PATCH 1/2] gnu: Add r-microbiome Mădălin Ionel Patrașcu
@ 2022-11-24 17:06 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2022-11-24 17:06 UTC (permalink / raw)
To: 56098-done
Applied and upgraded. Thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
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2022-06-19 20:39 [bug#56098] gnu: Add r-microbiome, r-ancombc MadalinIonel.Patrascu
2022-06-19 20:42 ` [bug#56098] [PATCH 1/2] gnu: Add r-microbiome Mădălin Ionel Patrașcu
2022-06-19 20:42 ` [bug#56098] [PATCH 2/2] gnu: Add r-ancombc Mădălin Ionel Patrașcu
2022-11-24 17:06 ` bug#56098: gnu: Add r-microbiome, r-ancombc Ricardo Wurmus
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