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gnu: Add r-doubletfinder.

* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
Ricardo Wurmus 2022-01-20 11:54:17 +01:00
parent 2b6af630d6
commit 61d7da5a1f
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1 changed files with 33 additions and 0 deletions

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