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@ -3762,3 +3762,39 @@ functions to perform a signature analysis with known signatures and a
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signature analysis on @dfn{stratified mutational catalogue} (SMC) are
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signature analysis on @dfn{stratified mutational catalogue} (SMC) are
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provided.")
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provided.")
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(license license:gpl3)))
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(license license:gpl3)))
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(define-public r-gcrma
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(package
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(name "r-gcrma")
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(version "2.54.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "gcrma" version))
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(sha256
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(base32
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"1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-affy" ,r-affy)
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("r-affyio" ,r-affyio)
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("r-biobase" ,r-biobase)
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("r-biocmanager" ,r-biocmanager)
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("r-biostrings" ,r-biostrings)
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("r-xvector" ,r-xvector)))
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(home-page "https://bioconductor.org/packages/gcrma/")
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(synopsis "Background adjustment using sequence information")
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(description
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"Gcrma adjusts for background intensities in Affymetrix array data which
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include optical noise and @dfn{non-specific binding} (NSB). The main function
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@code{gcrma} converts background adjusted probe intensities to expression
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measures using the same normalization and summarization methods as a
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@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
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to estimate probe affinity to NSB. The sequence information is summarized in
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a more complex way than the simple GC content. Instead, the base types (A, T,
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G or C) at each position along the probe determine the affinity of each probe.
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The parameters of the position-specific base contributions to the probe
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affinity is estimated in an NSB experiment in which only NSB but no
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gene-specific bidning is expected.")
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;; Any version of the LGPL
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(license license:lgpl2.1+)))
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