scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public
Resources
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 |
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=scfetch
to link to this page.