gnu: Add r-doubletfinder.
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
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@ -11613,6 +11613,39 @@ known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs
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can be calculated, and a number of descriptive plots easily generated.")
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can be calculated, and a number of descriptive plots easily generated.")
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(license license:artistic2.0)))
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(license license:artistic2.0)))
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(define-public r-doubletfinder
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(let ((commit "554097ba4e2c0ed7c28dc7f0b5b75277f3a50551")
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(revision "1"))
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(package
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(name "r-doubletfinder")
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(version (git-version "2.0.3" revision commit))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/chris-mcginnis-ucsf/DoubletFinder")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "1q1pnqw7ry4syp04wjmvz5bws6z4vg4c340ky07lk0vp577x2773"))))
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(properties `((upstream-name . "DoubletFinder")))
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(build-system r-build-system)
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(propagated-inputs (list r-fields r-kernsmooth r-rocr))
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(home-page "https://github.com/chris-mcginnis-ucsf/DoubletFinder")
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(synopsis "Identify doublets in single-cell RNA sequencing data")
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(description
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"DoubletFinder identifies doublets by generating artificial doublets
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from existing scRNA-seq data and defining which real cells preferentially
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co-localize with artificial doublets in gene expression space. Other
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DoubletFinder package functions are used for fitting DoubletFinder to
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different scRNA-seq datasets. For example, ideal DoubletFinder performance in
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real-world contexts requires optimal pK selection and homotypic doublet
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proportion estimation. pK selection is achieved using pN-pK parameter sweeps
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and maxima identification in mean-variance-normalized bimodality coefficient
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distributions. Homotypic doublet proportion estimation is achieved by finding
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the sum of squared cell annotation frequencies.")
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(license license:cc0))))
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(define-public gffread
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(define-public gffread
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;; We cannot use the tagged release because it is not in sync with gclib.
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;; We cannot use the tagged release because it is not in sync with gclib.
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;; See https://github.com/gpertea/gffread/issues/26
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;; See https://github.com/gpertea/gffread/issues/26
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