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:

Reference manual: scfetch.pdf
Vignettes: scfetch

Downloads:

Package source: scfetch_0.5.0.tar.gz
Windows binaries: r-prerel: scfetch_0.5.0.zip, r-release: scfetch_0.5.0.zip, r-oldrel: scfetch_0.5.0.zip
macOS binaries: r-prerel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): not available, r-prerel (x86_64): scfetch_0.5.0.tgz, r-release (x86_64): not available

Linking:

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