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Change-Id: I0eaefbaee0de6143fb892dda9c41459a5a5d30d6 --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) base-commit: 19c656e3cad3a4f1e3338a955a1af57e363545df diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f7f39f525d..391fb8e3a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -24342,6 +24342,52 @@ (define-public r-battenberg @url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}") (license license:gpl3))) +(define-public r-bayesprism + ;; The version string in the DESCRIPTION file was changed to 2.2.2 in this commit + (let ((commit "5d43190d5fdfc900571ae1b05b9dcad9ee6b8b2b") + (revision "2")) + (package + (name "r-bayesprism") + (version "2.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Danko-Lab/BayesPrism") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rlq6nv1adc9w1ync8834kv59ksixxzbpf3xlbxi5s8x54gv4q9y")))) + (properties `((upstream-name . "BayesPrism"))) + (build-system r-build-system) + (arguments + (list + #:phases '(modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ + (chdir "BayesPrism")))))) + (propagated-inputs (list r-biocparallel + r-gplots + r-matrix + r-nmf + r-scran + r-snowfall + r-r-utils)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/Danko-Lab/BayesPrism") + (synopsis "Bayesian cell type and gene expression deconvolution") + (description + "BayesPrism includes deconvolution and embedding learning modules. +The deconvolution module models a prior from cell type-specific expression +profiles from scRNA-seq to jointly estimate the posterior distribution of +cell type composition and cell type-specific gene expression from bulk +RNA-seq expression of tumor samples. The embedding learning module uses +Expectation-maximization (EM) to approximate the tumor expression using a +linear combination of malignant gene programs while conditional on the +inferred expression and fraction of non-malignant cells estimated by the +deconvolution module.") + (license license:gpl3)))) + (define-public r-catch (let ((commit "196ddd5a51b1a5f5daa01de53fdaad9b7505e084") (revision "1"))