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* [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

end of thread, other threads:[~2022-11-24 17:08 UTC | newest]

Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
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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