README.md

In rnabioco/clustifyrdata: External data sets for clustifyr

clustifyrdata

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 This repository has been archived.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

clustifyrdata provides 42 external data sets for cell-type assignment with clustifyr and reproducible scripts to build data objects.

Commonly used references:

| name | desc | ntypes | ngenes | org | from_pub | |:-----------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------|:-------|:------|:----------------------------------------------------------------------------| | ref_MCA | Mouse Cell Atlas | 713 | 8601 | mouse | from | | ref_tabula_muris_drop | Tabula Muris (10X) | 112 | 23341 | mouse | from | | ref_tabula_muris_facs | Tabula Muris (SmartSeq2) | 175 | 23341 | mouse | from | | ref_mouse.rnaseq | Mouse RNA-seq from 28 cell types | 28 | 21214 | mouse | from | | ref_moca_main | Mouse Organogenesis Cell Atlas (main cell types) | 37 | 26183 | mouse | from | | ref_immgen | Mouse sorted immune cells | 253 | 22134 | mouse | from | | ref_hema_microarray | Human hematopoietic cell microarray | 38 | 21246 | human | from | | ref_cortex_dev | Human cortex development scRNA-seq | 47 | 56864 | human | from | | ref_pan_indrop | Human pancreatic cell scRNA-seq (inDrop) | 14 | 20125 | human | from | | ref_pan_smartseq2 | Human pancreatic cell scRNA-seq (SmartSeq2) | 12 | 25525 | human | from |

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.