MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
f929ac3e2f3e45e0a6d512b14fac8452@mdc-berlin.de
gnu: Add r-microbiome, r-ancombc.
- 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 1/2] gnu: Add r-microbiome.
(address . 56098@debbugs.gnu.org)
20220619204201.18713-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-microbiome): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
Toggle diff (53 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/2] gnu: Add r-ancombc.
(address . 56098@debbugs.gnu.org)
20220619204201.18713-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-ancombc): New variable.
---
gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
Toggle diff (59 lines)
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
Ricardo Wurmus wrote 2 years ago
gnu: Add r-microbiome, r-ancombc.
(address . 56098-done@debbugs.gnu.org)
87r0xsmgc5.fsf@elephly.net
Applied and upgraded. Thanks!
--
Ricardo
Closed
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