dea_seurat - v2.0.2 - Minor fixes

• make all resource files input to rules

Full Changelog: https://github.com/epigen/dea_seurat/compare/v2.0.1...v2.0.2

- R
Published by sreichl about 1 year ago

dea_seurat - v2.0.1 - Enable module usage using `github()` directive

• improve DEA statistics bar plot
• improve continuity by enabling end-to-end compatibility with downstream modules
• to enable module usage using github() directive
  • source utils.R viaparamsinstead ofsnakemake@source`
  • comment global.yaml (now requires full snakemake installation, not minimal)
• add nodefaults to all env YAML

Full Changelog: https://github.com/epigen/dea_seurat/compare/v2.0.0...v2.0.1

- R
Published by sreichl over 1 year ago

dea_seurat - v2.0.0 - Snakemake 8 compatible

Breaking change: Requires Snakemake >= v8.20.1

Full Changelog: https://github.com/epigen/dea_seurat/compare/v1.0.1...v2.0.0

- R
Published by sreichl over 1 year ago

dea_seurat - v1.0.1 - stable version with complete docs and DOI

Release Notes v1.0.1

Documentation

• Link to Zenodo and document DOI.

Full Changelog: https://github.com/epigen/dea_seurat/compare/v1.0.0...v1.0.1

Release Notes v1.0.0

Features

• Differential Expression Analysis (DEA) using Seurat's FindMarkers or FindAllMarkers functions (parallelized).
  • Feature list generation per comparison group and direction (up/down) for downstream analysis.
  • Optional feature score tables per comparison group for downstream analyses.
  • Results filtered by statistical significance, effect size, and expression thresholds.
  • Filtered result statistics: number of statistically significant results split by effect direction.
• Visualizations
  • Bar plot of filtered result statistics showing the number of features and direction.
  • Volcano plots per comparison group highlighting features by configured significance and effect size cut-offs.
  • Hierarchically clustered heatmap of effect sizes for comparisons, with optional feature list usage.

Documentation

• Provided detailed usage tips for workflow execution.
• Example analysis using data from Lee et al (2020) on CRC samples, including runtime and example visualization.
• Recommended compatible MR.PARETO modules for upstream processing and downstream analyses.

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

- R
Published by sreichl over 2 years ago

dea_seurat - v1.0.0 - stable version with complete docs

Release Notes

Features

• Differential Expression Analysis (DEA) using Seurat's FindMarkers or FindAllMarkers functions (parallelized).
  • Feature list generation per comparison group and direction (up/down) for downstream analysis.
  • Optional feature score tables per comparison group for downstream analyses.
  • Results filtered by statistical significance, effect size, and expression thresholds.
  • Filtered result statistics: number of statistically significant results split by effect direction.
• Visualizations
  • Bar plot of filtered result statistics showing the number of features and direction.
  • Volcano plots per comparison group highlighting features by configured significance and effect size cut-offs.
  • Hierarchically clustered heatmap of effect sizes for comparisons, with optional feature list usage.

Documentation

• Provided detailed usage tips for workflow execution.
• Example analysis using data from Lee et al (2020) on CRC samples, including runtime and example visualization.
• Recommended compatible MR.PARETO modules for upstream processing and downstream analyses.

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

- R
Published by sreichl over 2 years ago