* 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
* 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
Applied and upgraded. Thanks! -- Ricardo