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Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
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Why does HPCA contain 'Neutrophil' and 'Neutrophils' #30

Closed PeteHaitch closed 5 years ago

PeteHaitch commented 5 years ago

Probably one for @friedue.

table(SingleR::HumanPrimaryCellAtlasData()$label.main)
#> 
#>            Astrocyte               B_cell                   BM 
#>                    2                   26                    7 
#>           BM & Prog.         Chondrocytes                  CMP 
#>                    1                    8                    2 
#>                   DC Embryonic_stem_cells    Endothelial_cells 
#>                   88                   17                   64 
#>     Epithelial_cells         Erythroblast          Fibroblasts 
#>                   16                    8                   10 
#>          Gametocytes                  GMP          Hepatocytes 
#>                    5                    2                    3 
#>           HSC_-G-CSF            HSC_CD34+            iPS_cells 
#>                   10                    6                   42 
#>        Keratinocytes           Macrophage                  MEP 
#>                   25                   90                    2 
#>             Monocyte                  MSC            Myelocyte 
#>                   60                    9                    2 
#> Neuroepithelial_cell              Neurons           Neutrophil 
#>                    1                   16                    3 
#>          Neutrophils              NK_cell          Osteoblasts 
#>                   18                    5                   15 
#>            Platelets     Pre-B_cell_CD34-     Pro-B_cell_CD34+ 
#>                    5                    2                    2 
#>        Pro-Myelocyte  Smooth_muscle_cells              T_cells 
#>                    2                   16                   68 
#>    Tissue_stem_cells 
#>                   55

Created on 2019-08-30 by the reprex package (v0.3.0)

Looking at how they get broken down in the 'fine' label:

                                         Neutrophil Neutrophils
  Neutrophil                                      3           3
  Neutrophil:commensal_E._coli_MG1655             0           2
  Neutrophil:GM-CSF_IFNg                          0           4
  Neutrophil:inflam                               0           4
  Neutrophil:LPS                                  0           4
  Neutrophil:uropathogenic_E._coli_UTI89          0           1

Should 'Neutrophil' and 'Neutrophils' be one 'main' label or is there a distinction I'm missing?

friedue commented 5 years ago

Nice catch! I'll defer to @dviraran

LTLA commented 5 years ago

I'm just going to rename it all to Neutrophils.