Various single-cell RNA-seq data on PBMC, generated by 10X Genomics.
1 2 3 4 5
Which PBMC dataset from 10X Genomics should be retrieved?
Logical, specifies whether the underlying HDF5 dataset should
be treated as sparse or not - will be passed to the call to
Single-cell RNA-seq and CITE-seq data were generated by 10X Genomics at various times, using different versions of CellRanger, different chemistries and different genome builds. For details, see the 10X website.
We obtained ‘filtered’ data and generated
SingleCellExperiment containers with data stored as an HDF5
rowData we include
are ENSEMBL gene ID and gene symbol provided by TENx genomics and a
remapping of the Ensembl identifier to a Hugo gene symbol as columns
Symbol using the
org.Hs.eg.db package. The difference
Symbol_TENx is that the former has many
missing values (for non-protein coding genes) whereas the later is
technically not a Hugo gene symbol.
In case of CITE-seq data, the
rowData has an additional column
Type specifying if the counts are "Gene Expression" or "Antibody Capture". Note that there is a separate
rowData for the
A SingleCellExperiment object with a HDF5Matrix in the
assay, which contains UMI counts for each gene in each cell.
Row- and column-level metadata are also provided.
In case of CITE-seq data, the "Antibody Capture" counts are stored in
altExp of the SingleCellExperiment.
Kasper D. Hansen, Stephanie Hicks, Davide Risso
10X Genomics (2017). 1.3 Million PBMC Cells from E18 Mice. https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.3.0/1M_neurons
1 2 3 4 5 6 7 8 9
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.