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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:

Framework

scfetch_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

Type Function Usage
Download and format fastq ExtractRun Extract runs with GEO accession number or GSM number
DownloadSRA Download sra files
SplitSRA Split sra files to fastq files and format to 10x standard style
Download and convert bam DownloadBam Download bam (support 10x original bam)
Bam2Fastq Convert bam files to fastq files
Download matrix and load to Seurat ExtractGEOMeta Extract sample metadata from GEO
ParseGEO Download matrix from GEO and load to Seurat
ExtractPanglaoDBMeta Extract sample metadata from PandlaoDB
ExtractPanglaoDBComposition Extract cell type composition of PanglaoDB datasets
ParsePanglaoDB Download matrix from PandlaoDB and load to Seurat
ShowCBDatasets Show all available datasets in UCSC Cell Browser
ExtractCBDatasets Extract UCSC Cell Browser datasets with attributes
ExtractCBComposition Extract cell type composition of UCSC Cell Browser datasets
ParseCBDatasets Download UCSC Cell Browser datasets and load to Seurat
Download objects ExtractZenodoMeta Extract sample metadata from Zenodo with DOIs
ParseZenodo Download rds/rdata/h5ad/loom from Zenodo with DOIs
ShowCELLxGENEDatasets Show all available datasets in CELLxGENE
ExtractCELLxGENEMeta Extract metadata of CELLxGENE datasets with attributes
ParseCELLxGENE Download rds/h5ad from CELLxGENE
ShowHCAProjects Show all available projects in Human Cell Atlas
ExtractHCAMeta Extract metadata of Human Cell Atlas projects with attributes
ParseHCA Download rds/rdata/h5/h5ad/loom from Human Cell Atlas
Convert between different single-cell objects ExportSeurat Convert SeuratObject to AnnData, SingleCellExperiment, CellDataSet/cell_data_set and loom
ImportSeurat Convert AnnData, SingleCellExperiment, CellDataSet/cell_data_set and loom to SeuratObject
SCEAnnData Convert between SingleCellExperiment and AnnData
SCELoom Convert between SingleCellExperiment and loom
Summarize datasets based on attributes StatDBAttribute Summarize datasets in PandlaoDB, UCSC Cell Browser and CELLxGENE based on attributes

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.


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.