GitHub - rnabioco/clustifyrdata: Reference data for cell-type assignment with clustifyr (original) (raw)
clustifyrdata
!!!! This repository has been archived. Please seeclustifyrdatahub. !!!!
clustifyrdata provides 42 external data sets for cell-type assignment with clustifyr andreproducible scriptsto 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 bySeurat.*_M3Drop
: variable genes used for dimension reduction as determined byM3Drop.
Installation
N.B.: clustifyrdata is a large data package (nearly 350 Mb uncompressed).
install.packages("pak")
pak::pkg_install("rnabioco/clustifyrdata")