StatescopeR

StatescopeR framework for discovery of cell states from cell type-specific gene expression profiles inferred from bulk mRNA profiles

Bioconductor version: 3.23 · Package version: 1.0.1

StatescopeR is an R wrapper around Statescope, a computational framework designed to discover cell states from cell type-specific gene expression profiles inferred from bulk RNA profiles.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("StatescopeR")

Details

Maintainer	Mischa Steketee <m.f.b.steketee@amsterdamumc.nl>
Author	Mischa Steketee [aut, cre] (ORCID: <https://orcid.org/0000-0001-7138-7554>), Bauke Ylstra [ths] (ORCID: <https://orcid.org/0000-0001-9479-3010>), Yongsoo Kim [ths] (ORCID: <https://orcid.org/0000-0002-2995-2131>), KWF Kankerbestrijding [fnd]
License	MIT + file LICENSE
URL	https://github.com/tgac-vumc/StatescopeR
Bug Reports	https://github.com/tgac-vumc/StatescopeR/issues
Downloads rank	57
Source branch	RELEASE_3_23
biocViews	Bayesian, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics

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Source package

Dependencies

Depends: R (>= 4.5.0)

Imports: S4Vectors, SummarizedExperiment, reticulate, methods, SingleCellExperiment, matrixStats, scran, basilisk, Matrix, ComplexHeatmap, ggplot2, cowplot, utils

Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, scRNAseq, scuttle, testthat