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envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-scDamAndTools): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) base-commit: 1b2d43fe016848ea2ec16ff18cbc14340944fc4e diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 51640b710f..03b1e81634 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2154,6 +2154,40 @@ (define-public python-pybedtools ;; licensed lgpl2.1+ (license (list license:expat license:lgpl2.1+)))) +(define-public python-scDamAndTools + (package + (name "python-scDamAndTools") + (version "1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KindLab/scDamAndTools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ;there are none + (propagated-inputs (list python-h5py + python-numpy + python-sortedcontainers + python-pandas + python-pysam + python-tqdm)) + (native-inputs (list python-cython python-pytest)) + (home-page "https://github.com/KindLab/scDamAndTools") + (synopsis "Functions for processing raw scDam&T-seq data") + (description + "This is a set of unctions for processing raw scDam&T-seq data. +A method to simultaneously measure protein-DNA interactions and transcription +from single cells (Rooijers et al., 2019). scDam&T-seq combines a DamID-based +method to measure protein-DNA interactions and an adaptation of CEL-Seq to +measure transcription. The starting point of the workflow is raw sequencing +data and the end result are tables of UMI-unique DamID and CEL-Seq counts.") + (license license:expat))) + (define-public python-bioframe (package (name "python-bioframe")