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 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("remotes") remotes::install_github("rnabioco/clustifyrdata")
