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Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a491f3d00..ecb60f2e24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16743,6 +16743,43 @@ ensemble machine learning for the estimation of nuisance functions.") visualizing bisulfite sequencing data.") (license license:artistic2.0))) +(define-public r-dada2 + (package + (name "r-dada2") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dada2" version)) + (sha256 + (base32 + "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + (properties `((upstream-name . "dada2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppparallel + r-reshape2 + r-shortread + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://benjjneb.github.io/dada2/") + (synopsis + "Accurate, high-resolution sample inference from amplicon sequencing data") + (description + "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs) +from high-throughput amplicon sequencing data, replacing the coarser and less +accurate OTU clustering approach. The dada2 pipeline takes as input +demultiplexed fastq files, and outputs the sequence variants and their +sample-wise abundances after removing substitution and chimera errors. +Taxonomic classification is available via a native implementation of the RDP +naive Bayesian classifier, and species-level assignment to 16S rRNA gene +fragments by exact matching.") + (license license:lgpl2.0))) + (define-public r-dmrseq (package (name "r-dmrseq") |