Baron et al. (2016) Human Pancreas Single-Cell RNA-Seq Reference Data
Source:R/data.R
RefCellData.RdA SingleCellExperiment object containing human pancreas single-cell RNA-seq data from Baron et al. (2016). This dataset serves as the reference dataset in the scLearn package for cell type annotation.
Format
A SingleCellExperiment object with 20125 genes (rows) and 8569 cells (columns). The object contains:
- counts
Raw count matrix
- logcounts
Log-normalized expression values
- colData
Cell metadata including:
cell_type1: Cell type annotations
other metadata fields...
References
Baron, M., Veres, A., Wolock, S. L., Faust, A. L., Gaujoux, R., Vetere, A., ... & Melton, D. A. (2016). A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell systems, 3(4), 346-360.
Examples
library(SingleCellExperiment)
data(RefCellData)
# Access expression matrix
assay(RefCellData, "logcounts")[1:5,1:5]
#> human3_lib2.final_cell_0129 human3_lib2.final_cell_0359
#> A1BG 0 0
#> A1CF 0 0
#> A2M 0 0
#> A2ML1 0 0
#> A4GALT 0 0
#> human3_lib1.final_cell_0076 human3_lib3.final_cell_0010
#> A1BG 0 0
#> A1CF 0 0
#> A2M 0 0
#> A2ML1 0 0
#> A4GALT 0 0
#> human3_lib1.final_cell_0096
#> A1BG 0
#> A1CF 0
#> A2M 0
#> A2ML1 0
#> A4GALT 0
# Access cell metadata
head(colData(RefCellData))
#> DataFrame with 6 rows and 30 columns
#> human cell_type1 total_features
#> <numeric> <factor> <integer>
#> human3_lib2.final_cell_0129 3 acinar 1974
#> human3_lib2.final_cell_0359 3 acinar 1571
#> human3_lib1.final_cell_0076 3 acinar 2699
#> human3_lib3.final_cell_0010 3 acinar 2648
#> human3_lib1.final_cell_0096 3 acinar 2728
#> human3_lib4.final_cell_0673 3 acinar 870
#> log10_total_features total_counts
#> <numeric> <integer>
#> human3_lib2.final_cell_0129 3.29557 11004
#> human3_lib2.final_cell_0359 3.19645 9013
#> human3_lib1.final_cell_0076 3.43136 12330
#> human3_lib3.final_cell_0010 3.42308 17228
#> human3_lib1.final_cell_0096 3.43600 13041
#> human3_lib4.final_cell_0673 2.94002 3178
#> log10_total_counts pct_counts_top_50_features
#> <numeric> <numeric>
#> human3_lib2.final_cell_0129 4.04159 56.3977
#> human3_lib2.final_cell_0359 3.95492 59.0259
#> human3_lib1.final_cell_0076 4.09100 43.6172
#> human3_lib3.final_cell_0010 4.23626 56.9886
#> human3_lib1.final_cell_0096 4.11534 44.1147
#> human3_lib4.final_cell_0673 3.50229 50.4405
#> pct_counts_top_100_features
#> <numeric>
#> human3_lib2.final_cell_0129 66.2577
#> human3_lib2.final_cell_0359 70.4427
#> human3_lib1.final_cell_0076 54.7040
#> human3_lib3.final_cell_0010 65.8695
#> human3_lib1.final_cell_0096 55.4482
#> human3_lib4.final_cell_0673 63.1215
#> pct_counts_top_200_features
#> <numeric>
#> human3_lib2.final_cell_0129 75.0091
#> human3_lib2.final_cell_0359 79.1967
#> human3_lib1.final_cell_0076 65.6285
#> human3_lib3.final_cell_0010 73.9784
#> human3_lib1.final_cell_0096 66.0532
#> human3_lib4.final_cell_0673 75.2045
#> pct_counts_top_500_features
#> <numeric>
#> human3_lib2.final_cell_0129 84.0876
#> human3_lib2.final_cell_0359 87.5846
#> human3_lib1.final_cell_0076 76.3747
#> human3_lib3.final_cell_0010 82.6503
#> human3_lib1.final_cell_0096 76.7733
#> human3_lib4.final_cell_0673 88.3575
#> total_features_endogenous
#> <integer>
#> human3_lib2.final_cell_0129 1974
#> human3_lib2.final_cell_0359 1571
#> human3_lib1.final_cell_0076 2699
#> human3_lib3.final_cell_0010 2648
#> human3_lib1.final_cell_0096 2728
#> human3_lib4.final_cell_0673 870
#> log10_total_features_endogenous
#> <numeric>
#> human3_lib2.final_cell_0129 3.29557
#> human3_lib2.final_cell_0359 3.19645
#> human3_lib1.final_cell_0076 3.43136
#> human3_lib3.final_cell_0010 3.42308
#> human3_lib1.final_cell_0096 3.43600
#> human3_lib4.final_cell_0673 2.94002
#> total_counts_endogenous
#> <integer>
#> human3_lib2.final_cell_0129 11004
#> human3_lib2.final_cell_0359 9013
#> human3_lib1.final_cell_0076 12330
#> human3_lib3.final_cell_0010 17228
#> human3_lib1.final_cell_0096 13041
#> human3_lib4.final_cell_0673 3178
#> log10_total_counts_endogenous pct_counts_endogenous
#> <numeric> <numeric>
#> human3_lib2.final_cell_0129 4.04159 100
#> human3_lib2.final_cell_0359 3.95492 100
#> human3_lib1.final_cell_0076 4.09100 100
#> human3_lib3.final_cell_0010 4.23626 100
#> human3_lib1.final_cell_0096 4.11534 100
#> human3_lib4.final_cell_0673 3.50229 100
#> pct_counts_top_50_features_endogenous
#> <numeric>
#> human3_lib2.final_cell_0129 56.3977
#> human3_lib2.final_cell_0359 59.0259
#> human3_lib1.final_cell_0076 43.6172
#> human3_lib3.final_cell_0010 56.9886
#> human3_lib1.final_cell_0096 44.1147
#> human3_lib4.final_cell_0673 50.4405
#> pct_counts_top_100_features_endogenous
#> <numeric>
#> human3_lib2.final_cell_0129 66.2577
#> human3_lib2.final_cell_0359 70.4427
#> human3_lib1.final_cell_0076 54.7040
#> human3_lib3.final_cell_0010 65.8695
#> human3_lib1.final_cell_0096 55.4482
#> human3_lib4.final_cell_0673 63.1215
#> pct_counts_top_200_features_endogenous
#> <numeric>
#> human3_lib2.final_cell_0129 75.0091
#> human3_lib2.final_cell_0359 79.1967
#> human3_lib1.final_cell_0076 65.6285
#> human3_lib3.final_cell_0010 73.9784
#> human3_lib1.final_cell_0096 66.0532
#> human3_lib4.final_cell_0673 75.2045
#> pct_counts_top_500_features_endogenous
#> <numeric>
#> human3_lib2.final_cell_0129 84.0876
#> human3_lib2.final_cell_0359 87.5846
#> human3_lib1.final_cell_0076 76.3747
#> human3_lib3.final_cell_0010 82.6503
#> human3_lib1.final_cell_0096 76.7733
#> human3_lib4.final_cell_0673 88.3575
#> total_features_feature_control
#> <integer>
#> human3_lib2.final_cell_0129 0
#> human3_lib2.final_cell_0359 0
#> human3_lib1.final_cell_0076 0
#> human3_lib3.final_cell_0010 0
#> human3_lib1.final_cell_0096 0
#> human3_lib4.final_cell_0673 0
#> log10_total_features_feature_control
#> <numeric>
#> human3_lib2.final_cell_0129 0
#> human3_lib2.final_cell_0359 0
#> human3_lib1.final_cell_0076 0
#> human3_lib3.final_cell_0010 0
#> human3_lib1.final_cell_0096 0
#> human3_lib4.final_cell_0673 0
#> total_counts_feature_control
#> <integer>
#> human3_lib2.final_cell_0129 0
#> human3_lib2.final_cell_0359 0
#> human3_lib1.final_cell_0076 0
#> human3_lib3.final_cell_0010 0
#> human3_lib1.final_cell_0096 0
#> human3_lib4.final_cell_0673 0
#> log10_total_counts_feature_control
#> <numeric>
#> human3_lib2.final_cell_0129 0
#> human3_lib2.final_cell_0359 0
#> human3_lib1.final_cell_0076 0
#> human3_lib3.final_cell_0010 0
#> human3_lib1.final_cell_0096 0
#> human3_lib4.final_cell_0673 0
#> pct_counts_feature_control total_features_ERCC
#> <numeric> <integer>
#> human3_lib2.final_cell_0129 0 0
#> human3_lib2.final_cell_0359 0 0
#> human3_lib1.final_cell_0076 0 0
#> human3_lib3.final_cell_0010 0 0
#> human3_lib1.final_cell_0096 0 0
#> human3_lib4.final_cell_0673 0 0
#> log10_total_features_ERCC total_counts_ERCC
#> <numeric> <integer>
#> human3_lib2.final_cell_0129 0 0
#> human3_lib2.final_cell_0359 0 0
#> human3_lib1.final_cell_0076 0 0
#> human3_lib3.final_cell_0010 0 0
#> human3_lib1.final_cell_0096 0 0
#> human3_lib4.final_cell_0673 0 0
#> log10_total_counts_ERCC pct_counts_ERCC
#> <numeric> <numeric>
#> human3_lib2.final_cell_0129 0 0
#> human3_lib2.final_cell_0359 0 0
#> human3_lib1.final_cell_0076 0 0
#> human3_lib3.final_cell_0010 0 0
#> human3_lib1.final_cell_0096 0 0
#> human3_lib4.final_cell_0673 0 0
#> is_cell_control
#> <logical>
#> human3_lib2.final_cell_0129 FALSE
#> human3_lib2.final_cell_0359 FALSE
#> human3_lib1.final_cell_0076 FALSE
#> human3_lib3.final_cell_0010 FALSE
#> human3_lib1.final_cell_0096 FALSE
#> human3_lib4.final_cell_0673 FALSE