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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-alpine): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..e0797206f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,46 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript abundance +in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million mapped reads). It +is currently designed for un-stranded paired-end RNA-seq data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder")