Table 1. Collection of datasets used for introducing and benchmarking clustifyr.

A description of single cell RNA-seq, bulk RNA-seq, and microarray datasets used in this study. The datasets available through ExperimentHub are references that were built from raw or downloaded data and can be used with clustifyr. R objects can be accessed using the direct download URLs to the .rda files, or through the clustifyrdatahub ExperimentHub.

Description	# of cell types	Organism	Publication	Source	Data Provider	R object download URL 1	Bioconductor ExperimentHubID 2	R object name 3
Mouse Cell Atlas	713	mouse	https://www.cell. com/cell/fulltext/S0092- 8674(18)30116-8	https://ndownloader.figshare.com/ files/10756795	figshare	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_MCA.rda	EH3444	ref_MCA
Tabula Muris (10X)	112	mouse	https://www.nature. com/articles/s41586- 018-0590-4	https://ndownloader.figshare.com/ articles/5821263	figshare	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_tabula_ muris_drop.rda	EH3445	ref_tabula_ muris_drop
Tabula Muris (SmartSeq2)	175	mouse	https://www.nature. com/articles/s41586- 018-0590-4	https://ndownloader.figshare.com/ articles/5821263	figshare	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_tabula_ muris_facs.rda	EH3446	ref_tabula_ muris_facs
Mouse RNA-seq from 28 cell types	28	mouse	https://genome. cshlp.org/content/ early/2019/03/11/ gr.240093.118	https://github.com/dviraran/ SingleR/tree/master/data	GitHub	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_mouse. rnaseq.rda	EH3447	ref_mouse. rnaseq
Mouse Organogenesis Cell Atlas (main cell types)	37	mouse	https://www.nature. com/articles/s41586- 019-0969-x	https://oncoscape.v3.sttrcancer. org/atlas.gs.washington.edu. mouse.rna/downloads	washington.edu	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_moca_ main.rda	EH3448	ref_moca_ main
Mouse sorted immune cells	253	mouse	https://www.nature. com/articles/ni1008- 1091	https://github.com/dviraran/ SingleR/tree/master/data	GitHub	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_immgen. rda	EH3449	ref_immgen
Human hematopoietic cell microarray	38	human	https://www.cell. com/fulltext/S0092- 8674(11)00005-5	https://ftp.ncbi.nlm.nih.gov/geo/ series/GSE24nnn/GSE24759/ matrix/GSE24759_series_matrix. txt.gz	GEO	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_hema_ microarray.rda	EH3450	ref_hema_ microarray
Human cortex development scRNA-seq	47	human	https://science. sciencemag.org/ content/358/6368/1318. long	https://cells.ucsc.edu/cortex-dev/ exprMatrix.tsv.gz	UCSC	https://github.com/ rnabioco/clustifyrdata/raw/ master/data/ref_cortex_ dev.rda	EH3451	ref_cortex_ dev
Human pancreatic cell scRNA-seq (inDrop)	14	human	https://www.cell. com/fulltext/S2405- 4712(16)30266-6	https://scrnaseq-public-datasets. s3.amazonaws.com/scater-objects/ baron-human.Rda	S3	https://github.com/ rnabioco/clustifyrdata/ raw/master/data/ref_pan_ indrop.rda	EH3452	ref_pan_ indrop
Human pancreatic cell scRNA-seq (SmartSeq2)	12	human	https://www. sciencedirect.com/ science/article/pii/ S1550413116304363	https://scrnaseq-public-datasets. s3.amazonaws.com/scater-objects/ segerstolpe.Rda	S3	https://github.com/ rnabioco/clustifyrdata/ raw/master/data/ref_pan_ smartseq2.rda	EH3453	ref_pan_ smartseq2
Human PBMCs, PBMC-Bench (multiple platforms)	9	human	https://doi.org/10.1186/ s13059-019-1795-z	https://zenodo.org/record/3357167/ files/scRNAseq_Benchmark_ datasets.zip?download=1	Zenodo	https://zenodo.org/ record/3357167/files/ scRNAseq_Benchmark_ datasets.zip?download=1	NA	NA
Human PBMCs, Unseen rejection test	5,7,10	human	https://doi.org/10.1186/ s13059-019-1795-z	https://zenodo.org/record/3357167/ files/scRNAseq_Benchmark_ datasets.zip?download=1	Zenodo	https://zenodo.org/ record/3357167/files/ scRNAseq_Benchmark_ datasets.zip?download=1	NA	NA
Mouse anterior lateral motor cortex (ALM)	34	mouse	https://doi.org/10.1038/ s41586-018-0654-5	https://portal.brain-map.org/ atlases-and-data/rnaseq/mouse- v1-and-alm-smart-seq	Allen Brain Institute	NA	NA	NA
Mouse brain primary visual cortex (VISp)	34	mouse	https://doi.org/10.1038/ s41586-018-0654-5	https://portal.brain-map.org/ atlases-and-data/rnaseq/mouse- v1-and-alm-smart-seq	Allen Brain Institute	NA	NA	NA
Human PBMC rejection test (SciBet)	5	human	https://doi.org/10.1038/ s41467-020-15523-2	http://scibet.cancer-pku.cn/ document.html	Investigator	NA	NA	NA
Human CBMC (CITE-Seq)	13	human	https://doi.org/10.1038/ nmeth.4380	ftp://ftp.ncbi.nlm.nih.gov/geo/ series/GSE100nnn/GSE100866/ suppl/GSE100866_CBMC_8K_ 13AB_10X-RNA_umi.csv.gz	GEO	NA	NA	NA
Human PBMCs (3k)	9	human	https://doi.org/10.1038/ ncomms14049	https://support.10xgenomics. com/single-cell-gene-expression/ datasets	10x Genomics	https://www.dropbox. com/s/63gnlw45jf7cje8/ pbmc3k_final.rds?dl=0	NA	NA

¹download URL to access R object (if available)

²R object id in the clustifyrdatahub Bioconductor Experiment hub

³R object name (if available via clustifyrdatahub)