MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
c88b9d89c0af48c5816bfcef153381f3@mdc-berlin.de
gnu: Add r-nada, r-zcompositions, r-aldex2.
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/3] gnu: Add r-zcompositions.
(address . 56021@debbugs.gnu.org)
20220616155721.23547-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-zcompositions): New variable.
---
gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
Toggle diff (44 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 28cd2e7fad..945cb5bdce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -836,6 +836,37 @@ (define-public r-dlm
known as Dynamic Linear Models.")
(license license:gpl2+)))
+(define-public r-zcompositions
+ (package
+ (name "r-zcompositions")
+ (version "1.4.0-1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "zCompositions" version))
+ (sha256
+ (base32
+ "1rrhja9iaq123r2gqw1bzrn1ri0s3z4wzq8p0sfcr1yb6pv13vik"))))
+ (properties `((upstream-name . "zCompositions")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-mass
+ r-nada
+ r-truncnorm))
+ (home-page "https://github.com/Japal/zCompositions")
+ (synopsis
+ "Treatment of zeros, left-censored and missing values in compositional data")
+ (description
+ "This package @code{zCompositions} is an @code{R} package for the imputation
+of left-censored data under a compositional approach. The implemented methods
+consider aspects of relevance for a compositional approach such as scale
+invariance, subcompositional coherence or preserving the multivariate relative
+structure of the data. Based on solid statistical frameworks, it comprises the
+ability to deal with single and varying censoring thresholds, consistent treatment
+of closed and non-closed data, exploratory tools, multiple imputation, @dfn{MCMC}
+(Markov Chain Monte Carlo), robust and non-parametric alternatives, and recent
+proposals for count data.")
+ (license license:gpl2+)))
+
(define-public r-zoo
(package
(name "r-zoo")
--
2.36.1
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 3/3] gnu: Add r-aldex2.
(address . 56021@debbugs.gnu.org)
20220616155721.23547-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-aldex2): New variable.
---
gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
Toggle diff (55 lines)
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")
--
2.36.1
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/3] gnu: Add r-nada.
(address . 56021@debbugs.gnu.org)
20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-nada): New variable.
---
gnu/packages/cran.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
Toggle diff (35 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b326332bf6..28cd2e7fad 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -27881,6 +27881,26 @@ (define-public r-nabor
to speed up repeated queries of the same set of target points.")
(license license:bsd-3)))
+(define-public r-nada
+ (package
+ (name "r-nada")
+ (version "1.6-1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "NADA" version))
+ (sha256
+ (base32
+ "0jp4mqr77cx7q5lff84s6wb0dwjy9mi0jyhbjc5fsx50bdczc3v7"))))
+ (properties `((upstream-name . "NADA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-survival))
+ (home-page "https://cran.r-project.org/package=NADA")
+ (synopsis "Nondetects and data analysis for environmental data")
+ (description
+ "This package contains methods described by Dennis Helsel in his book
+@emph{Nondetects and Data Analysis: Statistics for Censored Environmental Data}.")
+ (license license:gpl2+)))
+
(define-public r-naturalsort
(package
(name "r-naturalsort")
base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
--
2.36.1
Ricardo Wurmus wrote 2 years ago
gnu: Add r-nada, r-zcompositions, r-aldex2.
(address . 56021-done@debbugs.gnu.org)
87bkpn53x3.fsf@elephly.net
Applied, thank you!
--
Ricardo
Closed
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