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envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.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-atena): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..5ec69365d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,47 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-atena + (package + (name "r-atena") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atena" version)) + (sha256 + (base32 + "1jbnlxrk8npflym008cgrazamlsh6y624g1d6x648kcjd8zwvj6n")))) + (properties `((upstream-name . "atena"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-s4vectors + r-scales + r-sparsematrixstats + r-squarem + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/functionalgenomics/atena") + (synopsis "Analysis of transposable elements") + (description + "The @code{atena} package quantifies expression of @dfn{TEs} (transposable +elements) from RNA-seq data through different methods, including @code{ERVmap}, +@code{TEtranscripts} and @code{Telescope}. A common interface is provided to +use each of these methods, which consists of building a parameter object, calling +the quantification function with this object and getting a +@code{SummarizedExperiment} object as an output container of the quantified +expression profiles. The implementation allows quantifing TEs and gene +transcripts in an integrated manner.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion")