scfetch - Access and Format Single-cell RNA-seq Datasets from Public Resources

Introduction

scfetch is designed to accelerate users download and prepare single-cell datasets from public resources. It can be used to:

• Download fastq files from GEO/SRA, foramt fastq files to standard style that can be identified by 10x softwares (e.g. CellRanger).
• Download bam files from GEO/SRA, support downloading original 10x generated bam files (with custom tags) and normal bam files, and convert bam files to fastq files.
• Download scRNA-seq matrix and annotation (e.g. cell type) information from GEO, PanglanDB and UCSC Cell Browser, load the downnloaded matrix to Seurat.
• Download processed objects from Zeenodo, CELLxGENE and Human Cell Atlas.
• Formats conversion between widely used single cell objects (SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set and loom).

Framework

Installation

You can install the development version of scfetch from GitHub with:

# install.packages("devtools")
devtools::install_github("showteeth/scfetch")

For issues about installation, please refer INSTALL.md.

For data structures conversion, scfetch requires several python pcakages, you can install with:

# install python packages
conda install -c bioconda loompy anndata
# or
pip install anndata loompy

Usage

Vignette

Detailed usage is available in website.

Function list

Contact

For any question, feature request or bug report please write an email to songyb0519@gmail.com.

Code of Conduct

Please note that the scfetch project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.