spilterlize_integrate - v3.0.2 - minor fix

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v3.0.1...v3.0.2

- R
Published by sreichl 11 months ago

spilterlize_integrate - v3.0.1 - minor fixes

• Make all resource files input to rules

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v3.0.0...v3.0.1

- R
Published by sreichl about 1 year ago

spilterlize_integrate - v3.0.0 - New integration and confounding factor analysis features

Features - (Breaking change): Replaced reComBat with limma::removeBatchEffect for sample integration - Confounding factor analysis extension: Determined pairwise statistical association between all provided metadata per split to inform integration and downstream analyses such as linear modeling for differential expression analysis

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v2.0.2...v3.0.0

- R
Published by sreichl over 1 year ago

spilterlize_integrate - v2.0.2 - Minor fixes

What's Changed

• Bug fix: mask zero p-values with smallest observed p-value by @bednarsky in https://github.com/epigen/spilterlize_integrate/pull/22

New Contributors

• @bednarsky made their first contribution in https://github.com/epigen/spilterlize_integrate/pull/22

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

- R
Published by sreichl over 1 year ago

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

• to enable module usage using github() directive
  • comment global.yaml (now requires full snakemake installation, not minimal)
• add nodefaults to all env YAML

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

- R
Published by sreichl over 1 year ago

spilterlize_integrate - v2.0.0 - Snakemake 8 compatible

Breaking change: Requires Snakemake >= v8.20.1.

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v1.2.0...v2.0.0

- R
Published by sreichl over 1 year ago

spilterlize_integrate - v1.2.0 - Correlation Heatmaps

Features

• Correlation Heatmaps
  • Heatmap of sample-wise Pearson correlation matrix of the respective data split and processing step to quickly assess sample similarities e.g., replicates/conditions should correlate highly but batch should not.
  • Hierarchically clustered using method 'complete' with distance metric 'euclidean'.
  • Alphabetically sorted by sample name.

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v1.1.0...v1.2.0

- R
Published by sreichl almost 2 years ago

spilterlize_integrate - v1.1.0 - Confounding Factor Analysis

Features - Confounding Factor Analysis (CFA): Added a new feature to assess and visualize the statistical associations between metadata and principal components (PCs) using Kruskal-Wallis (categorical) and Kendall's Tau (numeric) tests, with results displayed as a heatmap of -log10 adjusted p-values. - Added VOOM normalization-specific Mean-Variance trend plot. - Improved visualization of the mean-variance relationship in the diagnostic plot using hexagonal heatmaps of 2d bin counts.

Bugfixes - fixed reComBat pip dependency issue using Snakemake's post-deployment script functionality.

Documentation - Tested on ATAC-seq count data from >200 samples. - Tested step-wise with minimal to maximal conjugations (i.e., from splitting up to integration). - Added other assays that could benefit from this module to the README. - Updated documentation with new features. - Added new visualizations to the Snakemake report.

Full Changelog: https://github.com/epigen/spilterlize_integrate/compare/v1.0.1...v1.1.0

- R
Published by sreichl about 2 years ago

spilterlize_integrate - fix CITATION.cff

- R
Published by sreichl almost 3 years ago

spilterlize_integrate - stable version with all features and complete documentation

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

- R
Published by sreichl almost 3 years ago