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

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Documentation for package ‘scfetch’ version 0.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Bam2Fastq	Convert bam files to fastq files.
DownloadBam	Download bam.
DownloadSRA	Download SRA.
ExportSeurat	Export SeuratObject to Other Formats.
ExtractCBComposition	Extract Cell Type Composition of UCSC Cell Browser Datasets.
ExtractCBDatasets	Extract UCSC Cell Browser Datasets with Attributes.
ExtractCELLxGENEMeta	Extract Metadata of CELLxGENE Datasets with Attributes.
ExtractGEOExp	Extract Raw Count Matrix or Fortmat Supplementary Files to 10x.
ExtractGEOExpSupp	Extract Raw Count Matrix from Supplementary Files.
ExtractGEOExpSupp10x	Fortmat Supplementary Files to 10x.
ExtractGEOExpSuppAll	Extract Raw Count Matrix from Supplementary Files or Fortmat Supplementary Files to 10x.
ExtractGEOInfo	Extract GEO Study Information.
ExtractGEOMeta	Extract Sample Metadata from GEO.
ExtractGEOSubMeta	Extract Sample Metadata.
ExtractHCAMeta	Extract Metadata of Human Cell Atlas Projects with Attributes.
ExtractPanglaoDBComposition	Extract Cell Type Composition of PanglaoDB Datasets.
ExtractPanglaoDBMeta	Extract Metadata of scRNA-seq Datasets in PanglaoDB.
ExtractRun	Extract Runs with GEO Accession Number or GSM Number.
ExtractZenodoMeta	Prepare Dataframe with Zenodo DOIs.
ImportSeurat	Convert Other Formats to SeuratObject.
PanglaoDBComposition	All Sample Composition of PanglaoDB Datasets
PanglaoDBMeta	All Sample Metadata of PanglaoDB Datasets
ParseCBDatasets	Download UCSC Cell Browser Datasets.
ParseCELLxGENE	Download CELLxGENE Datasets.
ParseGEO	Download Matrix from GEO and Load to Seurat.
ParseHCA	Download Human Cell Atlas Datasets.
ParsePanglaoDB	Parse PanglaoDB Data.
ParseZenodo	Download Data with Zenodo DOI.
SCEAnnData	Data Format Conversion between SingleCellExperiment and AnnData.
SCELoom	Data Format Conversion between SingleCellExperiment and loom.
ShowCBDatasets	Show All Available Datasets in UCSC Cell Browser.
ShowCELLxGENEDatasets	Show All Available Datasets in CELLxGENE.
ShowHCAProjects	Show All Available Projects in Human Cell Atlas.
SplitSRA	Split SRA to fastq Files and Format to 10x Standard Style.
StatDBAttribute	Stat Database Attributes.