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envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-agilp): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67ee6079c6..c0d874b423 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1664,6 +1664,50 @@ (define-public r-adamgui the @code{GFAGpathUi} function.") (license license:gpl2+))) +(define-public r-agilp + (package + (name "r-agilp") + (version "3.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "agilp" version)) + (sha256 + (base32 + "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp")))) + (properties `((upstream-name . "agilp"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/agilp") + (synopsis "Processing of Agilent expression array") + (description + "This package @code{agilp} was developed to provide a pipeline for the +low-level analysis of gene expression microarray data, primarily focused on the +Agilent platform, but which also provides utilities which may be useful for +other platforms. @code{Agilp} implements functions like: +@itemize +@item +@code{AAProcess}: extracts raw expression data from Agilent expression array +scanner files; +@item +@code{filenamex}: a file name listing utility; +@item +@code{Baseline}: constructs a file with the mean of each probe from a set of raw +expression array data files +@item +@code{Loader}: selects a set of processed array files from directory according +to criteria from a template file; +@item +@code{AALoess}: normalises a set of gene expression data files using @code{LOESS} +against a reference data set; +@item +@code{IDswop}: maps expression data across different bioinformatic identifiers; +@item +@code{Equaliser}: trims a set of gene expression data files to include only the +set of identifiers common to all files. +@end itemize") + ;; Some files are under GPLv2+ but the combined work is released under the + ;; GPLv3. + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder")