cluefish - cluefish v1.0.1

Main updates

• Included analysis of two external transcriptomic dose-response datasets in the analyses/ directory to provide further validation and testing of the Cluefish workflow
• Included additional scripts to reproduce the figures and tables for both external datasets from the associated paper
• Re-structured the analyses/ folder tree in general
• Updated clusterenrich() and simplenrich() functions to now compute enrichment ratios for functionally enriched biological functions
• Added download method choice for the dl_regulation_data() function to provide more flexibility
• Fixed issue in dataframe merging for both clustrfusion() and lonelyfishing()

Side-quests

• Enhanced documentation in scripts for reproducing results (figures and tables) from the associated paper
• Corrected subtle issues in table generation (e.g., selecting only GO:BP terms for the enrichment results, although KEGG and WP pathways were enriched)
• Added graphical abstract illustration from the associated paper to both the root README.md and vignette
• Applied minor fixes and text adjustements throughout the project

- R
Published by ellfran-7 9 months ago

cluefish - cluefish v1.0.0

• This is the first public release of the cluefish project.
• cluefish provides a streamlined workflow designed to enhance the biological interpretation of transcriptomic data series. Its goal is to capture a greater proportion of deregulated data considered for biological insights while improving the sensitivity of functional enrichment analysis. The latter enables the identification of smaller, more specific biological processes that might otherwise be overlooked.

- R
Published by ellfran-7 about 1 year ago