Available at http://bioconductor.org/packages/HCAData/.
This is an
R/ExperimentHub
package for accessing data from the Human Cell
Atlas as
SingleCellExperiment
objects.
The datasets can otherwise be downloaded from the Human Cell Atlas Data Portal, where they are available to the research community, either in raw format (with scripts to download the primary data), or in hdf5-based format (for the sets generated via the 10x method).
If you use the data, please refer to the original sources as well (plus the related publications, which will be listed here when they will be out), which are licensed under a Creative Commons Attribution 4.0 International License.
-
The
cellranger-processed data files and metadata were downloaded from the links provided in the Data Portal on November 5, 2018 -
This current release includes the following datasets:
| dataset.ID | subset | species | technology | cell.number | description |
|---|---|---|---|---|---|
| Census of Immune Cells | Umbilical cord blood | Homo sapiens | 10x | 384000 | Profiling of immunocytes by single cell RNA-seq for understanding human health and disease. |
| Census of Immune Cells | Bone marrow | Homo sapiens | 10x | 378000 | Profiling of immunocytes by single cell RNA-seq for understanding human health and disease. |
- Since the hdf5 files are derived from the cellranger pipeline, some information on their specific format can be found here
In this case, feel free to contact the author(s) of this package, and/or to provide a complete pull request with the recipe to add the missing dataset.
To get initial guidance for this, please refer to the excellent vignettes of the ExperimentHub package.
Please note that the HCAData project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.