In rnabioco/clustifyrdata: External data sets for clustifyr

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clustifyrdata

!!!! This repository has been archived. Please see clustifyrdatahub. !!!!

clustifyrdata provides r length(tools::list_files_with_type("data", type = "data")) external data sets for cell-type assignment with clustifyr and reproducible scripts to build data objects.

Commonly used references:

knitr::kable(clustifyrdata::downrefs)

See the reference page for available data sets, and individual ref download page. Additionally these datasets will be made available as a Bioconductor ExperimentHub (clustifyrdatahub)

Data sets have uniform prefixes / suffixes:

• ref_* : the prebuilt reference expression matrix.

• *_matrix : single-cell RNA expression matrix.

• *_avg : average expression caluculated from a single-cell RNA expression matrix.

• *_meta : metadata from a single-cell RNA-seq experiment.

• *_vargenes : variable genes used for dimension reduction, determined by Seurat.

• *_markers : marker genes determined by Seurat.

• *_M3Drop : variable genes used for dimension reduction as determined by M3Drop.

Installation

N.B.: clustifyrdata is a large data package (nearly 350 Mb uncompressed).

# install.packages("pak")
pak::pkg_install("rnabioco/clustifyrdata")

rnabioco/clustifyrdata documentation built on Nov. 8, 2022, 4:26 a.m.