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v1.0.1 - stable version with complete docs and DOI
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@sreichl sreichl released this 19 Feb 13:36
· 18 commits to master since this release
v1.0.1
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Release Notes v1.0.1

Documentation

  • Link to Zenodo and document DOI.

Full Changelog: v1.0.0...v1.0.1

Release Notes v1.0.0

Features

  • Preparation
    • Support for loading (multimodal) data from 10X Genomics Kits or MTX file format.
    • Optional addition of provided metadata to the Seurat object.
    • Assignment of Guide RNA and KO target genes for CRISPR Guide Capture data.
  • Merge & Split
    • Merging of all samples into one large Seurat object, including metadata.
    • Optional addition of externally provided metadata.
    • Splitting of merged data into subsets using metadata.
  • Filtering
    • Filtering of cells by a combination of logical expressions using metadata.
  • Pseudobulking
    • Pseudobulking based on user-specified metadata columns with options for aggregation methods.
    • Application of a cell count threshold to remove pseudobulked samples with fewer cells than specified.
  • Normalization
    • Normalization of gene expression data using SCTransform v2.
    • Normalization of all multimodal data using Centered Log-Ratio (CLR).
    • Dynamic determination of highly variable genes (HVGs).
  • Cell Scoring
    • Cell cycle scoring using Seurat::CellCycleScoring.
    • Gene module scoring using Seurat::AddModuleScore.
  • Correction
    • Normalization and correction for provided confounders using SCTransform v2.
  • Visualization
    • Support for Ridge-, Violin-, Dot-plots, and Heatmaps for various data modalities.
    • Metadata visualization after each processing step using inspectdf.
  • Save Counts
    • Functionality to save all counts as CSV after each processing step for all modalities.
  • Results Organization
    • Structured saving of results in the configured result path for easy access and analysis.

Documentation

  • Template for the Methods section of a scientific publication.
  • Detailed description of all features and tips for usage.
  • Configuration specifications are provided in the ./config/README.md and within config/config.yaml.
  • Example usage with a public scRNA-seq dataset consisting of 15 CRC samples, including instructions for data download.
  • Resources section with links to data resources for scRNA-seq data and recommended MR.PARETO modules for downstream analyses.

Full Changelog: https://github.com/epigen/scrnaseq_processing_seurat/commits/v1.0.0

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