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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:

  • 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

scfetch_framework

Installation

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

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

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.