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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-01-20 11:54:17 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-01-20 12:00:03 +0100 |
| commit | 61d7da5a1f5b082b55a55ab80242bdf3c283c653 (patch) | |
| tree | c44f4ac1ebd901fa4f2f9293ee9755fa4b57cf34 /gnu | |
| parent | 2b6af630d61dd5b16424be55088de2b079e9fbaf (diff) | |
| download | guix-61d7da5a1f5b082b55a55ab80242bdf3c283c653.tar.gz guix-61d7da5a1f5b082b55a55ab80242bdf3c283c653.zip | |
gnu: Add r-doubletfinder.
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6088a60a4..357baa289b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |