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The goal of 'scfetch' is to access and format single-cell RNA-seq datasets. It can be used to download single-cell RNA-seq datasets from widely used public resources, including GEO <https://www.ncbi.nlm.nih.gov/geo/>, Zenodo <https://zenodo.org/>, CELLxGENE <https://cellxgene.cziscience.com/>, Human Cell Atlas <https://www.humancellatlas.org/>, PanglaoDB <https://panglaodb.se/index.html> and UCSC Cell Browser <https://cells.ucsc.edu/>. And, it can also be used to perform object conversion between SeuratObject <https://satijalab.org/seurat/>, loom <http://loompy.org/>, h5ad <https://scanpy.readthedocs.io/en/stable/>, SingleCellExperiment <https://bioconductor.org/packages/release/bioc/html/scran.html>, CellDataSet <http://cole-trapnell-lab.github.io/monocle-release/> and cell_data_set <https://cole-trapnell-lab.github.io/monocle3/>.
| Version: | 0.5.0 |
| Depends: | R (≥ 2.10) |
| Imports: | Biobase, curl, data.table, dplyr, GEOquery, jsonlite, magrittr, Matrix, openxlsx, parallel, pbapply, purrr, rPanglaoDB, reticulate, Seurat, tibble, tools, utils, SingleCellExperiment, SummarizedExperiment, scater, LoomExperiment, httr, rlang, tidyr, methods |
| Suggests: | knitr, rmarkdown, scRNAseq, BiocStyle, htmltools, sceasy, SeuratDisk, SeuratWrappers, zellkonverter, GEOfastq |
| Published: | 2023-11-21 |
| Author: | Yabing Song [aut, cre] |
| Maintainer: | Yabing Song <songyb0519 at gmail.com> |
| BugReports: | https://github.com/showteeth/scfetch/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/showteeth/scfetch |
| NeedsCompilation: | no |
| Additional_repositories: | https://showteeth.github.io/drat/ |
| Materials: | README NEWS |
| CRAN checks: | scfetch results |
| Reference manual: | scfetch.pdf |
| Vignettes: |
scfetch |
| Package source: | scfetch_0.5.0.tar.gz |
| Windows binaries: | r-devel: scfetch_0.5.0.zip, r-release: scfetch_0.5.0.zip, r-oldrel: scfetch_0.5.0.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): scfetch_0.5.0.tgz, r-oldrel (x86_64): not available |
Please use the canonical form https://CRAN.R-project.org/package=scfetch to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.