diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d99a4e8ce..2bfca85bbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -6584,6 +6585,73 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'check 'remove-timestamps + (lambda _ + (with-directory-excursion + (string-append #$output "/site-library/Maaslin2/doc/demo_output/") + ;; Delete this log file with timestamps. + (delete-file "maaslin2.log") + ;; Replace PDF timestamps with an arbitrary fixed timestamp. + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* (find-files "." "\\.pdf$") + (("/CreationDate \\(D:.*\\)") + "/CreationDate (D:20230301143558)") + (("/ModDate \\(D:.*\\)") + "/ModDate (D:20230301143558)"))))))))) + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") |