GNU bug report logs - #56098
gnu: Add r-microbiome, r-ancombc.

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

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: gnu: Add r-microbiome, r-ancombc.
Date: Sun, 19 Jun 2022 20:39:53 +0000

[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Message #8 received at 56098 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56098 <at> debbugs.gnu.org>
Subject: [PATCH 1/2] gnu: Add r-microbiome.
Date: Sun, 19 Jun 2022 22:42:00 +0200

* 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

Message #11 received at 56098 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56098 <at> debbugs.gnu.org>
Subject: [PATCH 2/2] gnu: Add r-ancombc.
Date: Sun, 19 Jun 2022 22:42:01 +0200

* 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

Message #16 received at 56098-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 56098-done <at> debbugs.gnu.org
Subject: gnu: Add r-microbiome, r-ancombc.
Date: Thu, 24 Nov 2022 18:06:59 +0100

Applied and upgraded.  Thanks!

-- 
Ricardo

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