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https://github.com/federicomarini/hcadata
Access data from the Human Cell Atlas project, directly via R/Bioconductor
https://github.com/federicomarini/hcadata
bioconductor dataset experimenthub human-cell-atlas rna-seq single-cell-rna-seq
Last synced: 2 months ago
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Access data from the Human Cell Atlas project, directly via R/Bioconductor
- Host: GitHub
- URL: https://github.com/federicomarini/hcadata
- Owner: federicomarini
- License: other
- Created: 2018-11-05T15:56:17.000Z (about 6 years ago)
- Default Branch: devel
- Last Pushed: 2024-05-02T16:22:59.000Z (8 months ago)
- Last Synced: 2024-05-09T21:13:01.980Z (8 months ago)
- Topics: bioconductor, dataset, experimenthub, human-cell-atlas, rna-seq, single-cell-rna-seq
- Language: R
- Homepage: https://preview.data.humancellatlas.org
- Size: 7.37 MB
- Stars: 8
- Watchers: 4
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output:
md_document:
variant: markdown_github
---
[](https://github.com/federicomarini/HCAData/actions)
# HCAData
Available at http://bioconductor.org/packages/HCAData/.
This is an R/[ExperimentHub](https://bioconductor.org/packages/release/bioc/html/ExperimentHub.html) package for accessing data from the [Human Cell Atlas](https://www.humancellatlas.org) as [`SingleCellExperiment`](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) objects.
The datasets can otherwise be downloaded from the [Human Cell Atlas Data Portal](https://preview.data.humancellatlas.org), 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.
## Some additional information
- The [`cellranger`](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)-processed data files and metadata were downloaded from the links provided in [the Data Portal](https://preview.data.humancellatlas.org) on November 5, 2018
- This current release includes the following datasets:
```{r, eval = TRUE, echo = FALSE}
knitr::kable(
data.frame(
`dataset ID` = c("Census of Immune Cells","Census of Immune Cells"),
`subset` = c("Umbilical cord blood","Bone marrow"),
`species` = c("Homo sapiens","Homo sapiens"),
`technology` = c("10x", "10x"),
`cell number` = c(384000, 378000),
`description` = c("Profiling of immunocytes by single cell RNA-seq for understanding human health and disease.", "Profiling of immunocytes by single cell RNA-seq for understanding human health and disease.")
)
)
# maybe put a screenshot of iSEE viewing tSNE of each set?
```
- Since the hdf5 files are derived from the cellranger pipeline, some information on their specific format can be found [here](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)
## Some new dataset has been released but it is not in this package!
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](https://bioconductor.org/packages/release/bioc/html/ExperimentHub.html) package.
## Code of Conduct
Please note that the HCAData project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.