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| -rw-r--r-- | gnu/packages/bioconductor.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9d924c5429..f6917405a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -20025,6 +20025,41 @@ segmented data for individual and multiple arrays.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-snprelate + (package + (name "r-snprelate") + (version "1.34.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPRelate" version)) + (sha256 + (base32 + "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh")))) + (properties `((upstream-name . "SNPRelate"))) + (build-system r-build-system) + (propagated-inputs (list r-gdsfmt)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zhengxwen/SNPRelate") + (synopsis + "Toolset for relatedness and Principal Component Analysis of SNP data") + (description + "Genome-wide association studies (GWAS) are widely used to investigate +the genetic basis of diseases and traits, but they pose many computational +challenges. The R package SNPRelate provides a binary format for +single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic +Data Structure (GDS) data files. The GDS format offers the efficient +operations specifically designed for integers with two bits, since a SNP could +occupy only two bits. SNPRelate is also designed to accelerate two key +computations on SNP data using parallel computing for multi-core symmetric +multiprocessing computer architectures: Principal Component Analysis (PCA) and +relatedness analysis using Identity-By-Descent measures. The SNP GDS format +is also used by the GWASTools package with the support of S4 classes and +generic functions. The extended GDS format is implemented in the SeqArray +package to support the storage of single nucleotide variations (SNVs), +insertion/deletion polymorphism (indel) and structural variation calls in +whole-genome and whole-exome variant data.") + (license license:gpl3))) + (define-public r-snpstats (package (name "r-snpstats") |