NEWS.md

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

scfetch 0.5.0

New features

• Added ExtractCELLxGENEMeta to extract metadata of CELLxGENE datasets.
• Added ParseCELLxGENE to download objects from CELLxGENE.
• Added ExtractHCAMeta to extract metadata of Human Cell Atlas projects.
• Added ShowHCAProjects to show all available Human Cell Atlas projects.
• Added ShowCELLxGENEDatasets to show all available CELLxGENE datasets.
• Added StatDBAttributeto stat database attributes.
• Added ParseHCA to download objects from Human Cell Atlas.

Minor changes

• Added filters to ExtractCELLxGENEMeta.
• Added data.type in ParseGEO to return count matrix for bulk RNA-seq.
• Added filters to ExtractHCAMeta.
• Added catalog in ShowHCAProjects.
• Fixed bug in ParseCELLxGENE and returned failed dataframe when downloading error.
• Fixed bug in ImportSeurat.
• Fixed bug in ExportSeurat.
• Resolved installation.
• Fixed bug in ExtractZenodoMeta (API changed).
• Fixed bug in ShowCBDatasets (added --no-check-certificate when downloading json files).
• Fixed bug in ShowCELLxGENEDatasets.

scfetch 0.4.0

New features

• Added ExportSeurat to convert SeuratObject to other scRNA-seq formats.
• Added ImportSeurat to convert other scRNA-seq formats to SeuratObject.
• Added SCEaAnnData to perform data format conversion between SingleCellExperiment and AnnData.
• Added SCELoom to perform data format conversion between SingleCellExperiment and loom.
• Added ExtractPanglaoDBComposition to extract cell type composition of PanglaoDB datasets.

Minor changes

• Added conda.path in ExportSeurat to specify conda enviroment used.
• Fixed bug in SCELoom to keep gene names and cell ID.
• Bam2Fastq supported normal bam files (non-10x bam files).
• Changed function names: ShowPanglaoDBMeta to ExtractPanglaoDBMeta, PrepareZenodo to ExtractZenodoMeta.
• Supported downloadding normal (non-10x) bam file in DownloadBam.
• ExtractZenodoMeta supported a vector of Zenodo dois.
• Added fastq.type in SplitSRA to deal with fastq files from 10x, other scRNA-seq protocols and bulk RNA-seq.
• Added check for split.cmd.paras in SplitSRA.
• Added local.data in ExtractPanglaoDBMeta and ExtractPanglaoDBComposition to use cached sample metadata and composition.

scfetch 0.3.0

New features

• Added ExtractRun to extract run number from GEO.
• Added DownloadSRA to download SRA according to run number.
• Added SplitSRA to split SRA to fastqs and format the fastqs to 10x format.
• Added DownloadBam to download 10x bam files from GEO.
• Added Bam2Fastq to convert bam to 10x formatted fastqs.

Minor changes

• Fixed bug in DownloadSRA when downloading bam files.

scfetch 0.2.0

New features

• Provided APIs for GEO.
• Added Read10XOnline to load cellranger output.
• Added ExtractCBComposition to extract cell type composition of UCSC Cell Browser datasets.
• ParseGEO support creating Seurat object.
• Added ExtractGEOMeta to support extract metadata from GEO.

Minor changes

• Supported lazy mode in ShowCBDatasets to save time for multi-runs.
• Optimized the paras for ExtractCBDatasets and ParseCBDatasets.
• Added cell.num filter to ParseCBDatasets, ExtractCBDatasets and ShowPanglaoDBMeta.
• Extracted matrix, barcode and feature info from dataset.json (comprehensive) instead of desc.json.
• Fixed bugs in ParseCBDatasets when dealing with cellranger output.
• Added timeout in ParseCBDatasets to avoid possible timeout error.
• Changed time.out in GEO related functions to timeout.
• Simplified the output of ParseGEO.
• Fixed bug in ExtractGEOMeta.

scfetch 0.1.0

• Provided APIs for Zenodo, PanglaoDB and UCSC Cell Browser.

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.