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v1.0.0 - stable version with new features, complete docs and examples
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@sreichl sreichl released this 12 Jun 17:04
· 15 commits to main since this release
v1.0.0
60dfa07

Features

  • Enrichment Analysis Methods:

    • Region Set Analysis:
      • LOLA: Genomic Locus Overlap Enrichment Analysis.
      • GREAT: Genomic Regions Enrichment of Annotations Tool using rGREAT.
      • pycisTarget: Motif enrichment analysis in region sets to identify high-confidence transcription factor (TF) cistromes.
    • Gene Set Analysis:
      • Over-representation Analysis (ORA): Using GSEApy's enrich() function.
      • RcisTarget: Motif enrichment analysis in gene sets to identify high-confidence TF cistromes.
    • Region-based Gene Set Analysis:
      • Region-gene associations obtained using (r)GREAT.
      • Complementary ORA using GSEApy and TFBS motif enrichment analysis using RcisTarget.
    • Preranked Gene Set Analysis:
      • Preranked GSEA using GSEApy's prerank() function.

  • Database Support:

    • Local databases for GSEApy and (r)GREAT
      • GMT files e.g., from MSigDB or Enrichr.
      • (custom) JSON file support.
    • LOLA databases from LOLA Region Databases or custom created.
    • cisTarget databases for pycisTarget and RcisTarget.

  • Group Aggregation:

    • Aggregation of results per method and database.
    • Filtered aggregation retaining only statistically significant terms.

  • Visualization:

    • Enrichment dot plots for each query, method, and database combination.
    • Hierarchically clustered heatmaps and bubble plots for group summaries.

Documentation

  • Usage Instructions:

    • Steps to download relevant databases and configure the analysis.
    • Commands for running the workflow and generating reports.

  • Examples: Provided example queries and databases with instructions for running a complete analysis.

  • Links and Resources:

    • GitHub repository, Zenodo repository, and Snakemake Workflow Catalog entry.
    • Recommended compatible MR.PARETO modules for upstream processing and analyses.
    • Web versions of some tools and databases for region/gene sets.

Beware: All packages got updated/changed to their latest versions, therefore results might differ. If possible, rerunning is recommended. The workflow expanded its functionality significantly, hence many changes were introduced especially in the configuration.

Thanks to early adopters @dariarom94, @Rubbert, and @bednarsky for testing and providing constructive feedback.

Bug fixes and performance improvements are not mentioned.

Full Changelog: v0.1.1...v1.0.0

Contributors

Rubbert, dariarom94, and bednarsky
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