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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-03-29 22:18:49 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-30 08:55:45 +0100 |
| commit | e99380d67b459128807f27184b93f0b2a9e6c3fd (patch) | |
| tree | a33ae2ed0716f624854ff4d001c25d9f1ad0b457 | |
| parent | 303f2ed1c6447bd01e5310ea16aec6cbd0153a5b (diff) | |
| download | patches-e99380d67b459128807f27184b93f0b2a9e6c3fd.tar patches-e99380d67b459128807f27184b93f0b2a9e6c3fd.tar.gz | |
gnu: Add r-gcrma.
* gnu/packages/bioconductor.scm (r-gcrma): New variable.
| -rw-r--r-- | gnu/packages/bioconductor.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4c31ffcc0d..91a5a66ec2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3762,3 +3762,39 @@ functions to perform a signature analysis with known signatures and a signature analysis on @dfn{stratified mutational catalogue} (SMC) are provided.") (license license:gpl3))) + +(define-public r-gcrma + (package + (name "r-gcrma") + (version "2.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gcrma" version)) + (sha256 + (base32 + "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-biostrings" ,r-biostrings) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/gcrma/") + (synopsis "Background adjustment using sequence information") + (description + "Gcrma adjusts for background intensities in Affymetrix array data which +include optical noise and @dfn{non-specific binding} (NSB). The main function +@code{gcrma} converts background adjusted probe intensities to expression +measures using the same normalization and summarization methods as a +@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information +to estimate probe affinity to NSB. The sequence information is summarized in +a more complex way than the simple GC content. Instead, the base types (A, T, +G or C) at each position along the probe determine the affinity of each probe. +The parameters of the position-specific base contributions to the probe +affinity is estimated in an NSB experiment in which only NSB but no +gene-specific bidning is expected.") + ;; Any version of the LGPL + (license license:lgpl2.1+))) |