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Date: Tue, 12 Apr 2022 23:57:55 +0200 Message-ID: <20220412215755.8819-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-AS-Result: No-10-3.581000-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEBkr LtyHdvykBpzxkixO8HnuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHOSL mthZG++ZtIzAkBnbNUvA+7o7FdzRRg7YNOTN1RNUA13wM4W57IRtXMWL63O8vIiqlmO0FgHt7/p 60BYoiFXCjkqXcbv0bB7aHw6Yd9y4sm617PZ0pZ+LzNWBegCW2wgn7iDBesS3CttcwYNipX7Pc2 SM55IWTwMKXdJqwi281QTmmn4K4NN/gKGNk3PcG9NdFfjVXeTzMrFRgGfC2cNPSjkuxmNhf2lJE rfutdtClfdMQSTDSzwzGDifJzsMFKEIODKywTy6jfJglXzHQ6sxRVzSzXt2xg0t1kxIt39BVyvb Tg/runA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-3.581000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-SNTS-SMTP: E6B66CC5190E08113F5A30D4F9C9CF94A330EFD4A33DC627735FBF43CBE86FB92000:F Received-SPF: pass client-ip=194.95.238.172; 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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-absseq): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..25e02bebad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1139,6 +1139,35 @@ (define-public r-abadata All datasets are restricted to protein coding genes.") (license license:gpl2+))) +(define-public r-absseq + (package + (name "r-absseq") + (version "1.48.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ABSSeq" version)) + (sha256 + (base32 + "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650")))) + (properties `((upstream-name . "ABSSeq"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-locfit)) + (home-page "https://bioconductor.org/packages/ABSSeq") + (synopsis + "RNA-Seq analysis based on modelling absolute expression differences") + (description + "This package @code{ABSSeq} implements a new RNA-Seq analysis method and +integrates two modules: a basic model for pairwise comparison and a linear +model for complex design. RNA-Seq quantifies gene expression with reads count, +which usually consists of conditions (or treatments) and several replicates for +each condition. This software infers differential expression directly by the +counts difference between conditions. It assumes that the sum counts +difference between conditions follow a negative binomial distribution. In +addition, @code{ABSSeq} moderates the fold-changes by two steps: the expression +level and gene-specific dispersion, that might facilitate the gene ranking by +fold-change and visualization.") + (license license:gpl3+))) + (define-public r-aneufinderdata (package (name "r-aneufinderdata") -- 2.34.0