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[bug#56098,2/2] gnu: Add r-ancombc.

Message ID 20220619204201.18713-2-madalinionel.patrascu@mdc-berlin.de
State New
Headers show
Series [bug#56098,1/2] gnu: Add r-microbiome. | expand


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Mădălin Ionel Patrașcu June 19, 2022, 8:42 p.m. UTC
* gnu/packages/bioconductor.scm (r-ancombc): New variable.
 gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
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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
     (name "r-aneufinder")