Package: scfetch

Type: Package

Title: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Version: 0.7.0

Authors@R:

person(given = "Yabing",

family = "Song",

role = c("aut", "cre"),

email = "songyb0519@gmail.com")

Maintainer: Yabing Song <songyb0519@gmail.com>

Description: 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/>.

License: GPL (>= 3)

Encoding: UTF-8

LazyData: true

RoxygenNote: 7.2.3

biocViews:

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,

DESeq2

Suggests:

knitr,

rmarkdown,

scRNAseq,

BiocStyle,

htmltools,

sceasy,

SeuratDisk,

SeuratWrappers,

zellkonverter,

GEOfastq,

cellxgene.census

VignetteBuilder: knitr

Additional_repositories: https://showteeth.github.io/drat/

URL: https://github.com/showteeth/scfetch

BugReports: https://github.com/showteeth/scfetch/issues

Depends:

R (>= 2.10)