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[bug#56021,3/3] gnu: Add r-aldex2.

Message ID 20220616155721.23547-3-madalinionel.patrascu@mdc-berlin.de
State New
Headers
Series [bug#56021,1/3] gnu: Add r-nada. |

Commit Message

Mădălin Ionel Patrașcu June 16, 2022, 3:57 p.m. UTC 
* gnu/packages/bioconductor.scm (r-aldex2): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
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Patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..3abd57359d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,48 @@  (define-public r-agimicrorna
 objects are used so that other packages could be used as well.")
     (license license:gpl3)))
 
+(define-public r-aldex2
+  (package
+    (name "r-aldex2")
+    (version "1.28.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ALDEx2" version))
+              (sha256
+               (base32
+                "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"))))
+    (properties `((upstream-name . "ALDEx2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-genomicranges
+           r-iranges
+           r-multtest
+           r-rfast
+           r-s4vectors
+           r-summarizedexperiment
+           r-zcompositions))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ggloor/ALDEx_bioc")
+    (synopsis
+     "Analysis Of differential abundance taking sample variation into account")
+    (description
+     "This package provides a differential abundance analysis for the comparison
+of two or more conditions.  Useful for analyzing data from standard RNA-seq or
+meta-RNA-seq assays as well as selected and unselected values from in-vitro
+sequence selections.  Uses a Dirichlet-multinomial model to infer abundance from
+counts, optimized for three or more experimental replicates.  The method infers
+biological and sampling variation to calculate the expected false discovery
+rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test
+(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear
+model (via aldex.glm), or a correlation test (via aldex.corr).  All tests report
+p-values and Benjamini-Hochberg corrected p-values.  ALDEx2 also calculates
+expected standardized effect sizes for paired or unpaired study designs.")
+    ;; The code for the function "rdirichlet" which is from the "R" package
+    ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball
+    ;; LICENSE specifies GPL-3.
+    (license (list license:agpl3+ license:gpl2+ license:gpl3))))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")