Skip to contents

Changelog

Source: NEWS.md

GEfetch2R 0.7.3

Major changes

  • Added LoadRData to load objects, count matrix, and metadata from RData.
  • Added CheckAPI to check the availability of APIs.
  • Supported loading and downloading a given dataset/collection/project from CELLxGENE, Human Cell Atlas, UCSC Cell Browser, PanglaoDB.
  • Supported multiple runs in RunCellRanger, RunSTAR, Fastq2R .
  • LoadRData supported SeuratObject generated by Seurat v5.

Minor changes

  • Fix bug in ImportSeurat.
  • Fix bug in LoadRData.
  • Fix API changes in CELLxGENE and Human Cell Atlas.
  • Fix bugs in ParseCELLxGENE.
  • Fix bugs in ExtractRun when a sample has multiple runs.
  • Fix bugs in Fastq2R when a sample has multiple runs.
  • Add wget in DownloadBam, DownloadFastq and DownloadSRA.
  • Fix bug in ParseGEO when 10X data contains more than one type.
  • Fix bug in scientific notation (36000000 -> 3.6e+07).
  • Add skip.gsm in DownloadFastq2R to control used GSM.
  • Fix bug in Bam2Fastq.
  • Fix bug in ImportSeurat.
  • Fix bug in Fastq2R when loading to Seurat.
  • Change PanglanDB to PanglaoDB (spelling mistake).

GEfetch2R 0.7.2

Major changes

  • Large-scale evaluation:
    • Load count matrix generated by featureCounts from GEO (smart-seq2)
    • Load count matrix with extra columns from GEO (smart-seq2)
    • Load count matrix generated by STAR from GEO (smart-seq2)
    • Load count matrix in mixed file formats from GEO (smart-seq2)
    • Load count matrix in h5 format from GEO (10x)
    • Compressed files (zip, tar.gz, tar) in downloaded supplemental files (GEO, 10x)
    • Sample name is after the fixed name (GEO, 10x)
  • Change the way of downloading supplemental files with index from GEO.
  • Extract metadata from supplemental files (GEO).
  • Added ParseGEOProcessed to download processed objects from GEO.

Minor changes

  • Removed cellxgene.census dependency to avoid possible installation issue on Windows.
  • Fix bug in MoveFileRecursively.

GEfetch2R 0.7.1

New features

  • Added Seu2AD/SCE2AD/AD2Seu/AD2SCE for benchmark (data IO).

Minor changes

  • Added timeout in ShowCBDatasets.
  • Added Gunzip to deal with the removal of gunzip in package GEOquery.

GEfetch2R 0.7.0

New features

  • Added DownloadFastq to download FASTQ files directly from ENA.
  • Updated DownloadSRA to download sra files directly from ENA.
  • Updated DownloadBam to download bam files directly from ENA.

Minor changes

  • Updated DownloadSRA, DownloadFastq, DownloadBam to keep the same file structure.
  • Updated DownloadFastq to format the fastqs to 10x format.

GEfetch2R 0.6.1

  • Fix bugs in LoadRDS2Seurat.
  • Give a message when there is no file with file.ext in ParseHCA, ParseHCA, ExtractZenodoMeta, ParseZenodo.
  • Return SeuratObject in ParseHCA.
  • Fix bug in Load2Seurat.
  • Support pigz in Bam2Fastq.
  • Return full dataframe in ExtractRun.
  • Fix bug in ParseCELLxGENE, ParseHCA.
  • Add use.cores in ParseCELLxGENE, ParseHCA, ParseZenodo.
  • Fix bug in ExtractGEOMeta.

GEfetch2R 0.6.0

New features

  • Added RunCellRanger to run CellRanger on downloaded FASTQ files.
  • Added RunSTAR to run STAR on downloaded FASTQ files.
  • Added Fastq2R to pipe FASTQ files to SeuratObject and DESeqDataSet.
  • Updated StatDBAttribute to support cellxgene.census.
  • Updated ParseCELLxGENE to support cellxgene.census and return SeuratObject.
  • Updated ParseCBDatasets to support subset.

Minor changes

  • Return DESeqDataSet when data.type is bulk in ParseGEO.
  • Support summarising multiple attributes in StatDBAttribute.
  • Fix bugs in mergeExperiments.
  • Fix bugs in ParseHCA (no file with extension specified by file.ext).
  • Optimize ParseHCA to return metadata of downloaded files.

GEfetch2R 0.5.1

  • Create output directory automatically.
  • CELLxGENE new API.

GEfetch2R 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.
  • docker image added.

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.
  • Supported GEO of 10x (separate files).

GEfetch2R 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.

GEfetch2R 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.

GEfetch2R 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 SeuratObject.
  • 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.

GEfetch2R 0.1.0

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