README.md
In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

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

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).

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

Detailed usage is available in website.

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

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

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.