| Title: | External data sets for clustifyr in ExperimentHub |
|---|---|
| Description: | References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr <https://bioconductor.org/packages/clustifyr> to assign cell type identities. |
| Authors: | Rui Fu [aut] (ORCID: <https://orcid.org/0000-0001-8183-4549>), Kent Riemondy [aut, cre] (ORCID: <https://orcid.org/0000-0003-0750-1273>), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (ORCID: <https://orcid.org/0000-0003-2928-6308>), Jay Hesselberth [ctb] (ORCID: <https://orcid.org/0000-0002-6299-179X>), Sidhant Puntambekar [ctb] |
| Maintainer: | Kent Riemondy <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.22.0 |
| Built: | 2026-10-10 11:14:52 UTC |
| Source: | https://github.com/bioc/clustifyrdatahub |
47 distinct annotated clusters of human neuronal subtypes
ref_cortex_devref_cortex_dev
An object of class function of length 1.
<https://cells.ucsc.edu/?ds=cortex-dev#>
Other ref:
ref_MCA(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_cortex_dev(metadata = TRUE)ref_cortex_dev(metadata = TRUE)
38 distinct purified populations of human hematopoietic cells
ref_hema_microarrayref_hema_microarray
An object of class function of length 1.
[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24759]
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_hema_microarray(metadata = TRUE)ref_hema_microarray(metadata = TRUE)
253 mouse immune cell types
ref_immgenref_immgen
An object of class function of length 1.
["SingleR"]
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_immgen(metadata = TRUE)ref_immgen(metadata = TRUE)
from mouse cell atlas project
ref_MCAref_MCA
An object of class function of length 1.
<https://figshare.com/s/865e694ad06d5857db4b>
Other ref:
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_MCA(metadata = TRUE)ref_MCA(metadata = TRUE)
100,000 cells
ref_moca_mainref_moca_main
An object of class function of length 1.
<http://atlas.gs.washington.edu/mouse-rna/>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_moca_main(metadata = TRUE)ref_moca_main(metadata = TRUE)
Data aggregated from NCBI Gene Expression Omnibus
ref_mouse_atlasref_mouse_atlas
An object of class function of length 1.
<https://github.com/rnabioco/scRNA-seq-Cell-Ref-Matrix/blob/master/atlas/musMusculus/MouseAtlas.rds>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_mouse_atlas(metadata = TRUE)ref_mouse_atlas(metadata = TRUE)
28 general cell types
ref_mouse.rnaseqref_mouse.rnaseq
An object of class function of length 1.
["SingleR"]
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_mouse.rnaseq(metadata = TRUE)ref_mouse.rnaseq(metadata = TRUE)
A sample of 8569 pancreas cells
ref_pan_indropref_pan_indrop
An object of class function of length 1.
<https://hemberg-lab.github.io/scRNA.seq.datasets/human/pancreas/>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_smartseq2(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_pan_indrop(metadata = TRUE)ref_pan_indrop(metadata = TRUE)
A sample of 2209 pancreas cells
ref_pan_smartseq2ref_pan_smartseq2
An object of class function of length 1.
<https://hemberg-lab.github.io/scRNA.seq.datasets/human/pancreas/>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_tabula_muris_drop(),
ref_tabula_muris_facs()
ref_pan_smartseq2(metadata = TRUE)ref_pan_smartseq2(metadata = TRUE)
422,803 droplet libraries, 55,656 of which passed a QC cutoff of 500 genes and 1000 UMI
ref_tabula_muris_dropref_tabula_muris_drop
An object of class function of length 1.
<https://tabula-muris.ds.czbiohub.org/>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_facs()
ref_tabula_muris_drop(metadata = TRUE)ref_tabula_muris_drop(metadata = TRUE)
53,760 cells from 20 tissues from 8 mice
ref_tabula_muris_facsref_tabula_muris_facs
An object of class function of length 1.
<https://tabula-muris.ds.czbiohub.org/>
Other ref:
ref_MCA(),
ref_cortex_dev(),
ref_hema_microarray(),
ref_immgen(),
ref_moca_main(),
ref_mouse.rnaseq(),
ref_mouse_atlas(),
ref_pan_indrop(),
ref_pan_smartseq2(),
ref_tabula_muris_drop()
ref_tabula_muris_facs(metadata = TRUE)ref_tabula_muris_facs(metadata = TRUE)