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 This repository has been archived.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.

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.

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

pak::pkg_install("rnabioco/clustifyrdata")