NEWS
TFEA.ChIP 1.29.4
New Features
- Added a meta-analysis function to combine results across datasets.
- Introduced a new wrapper function that performs the full enrichment workflow in one step, reducing manual intervention.
Enhancements
- Refactored and optimized several core functions for improved performance.
- Improved plotting functions for clearer and more customizable visualizations.
Data Updates
- Updated the ChIPDB object using newly available regulatory region-to-gene annotations from the ENCODE rE2G method and CREdb, enhancing the biological relevance and accuracy of TF-gene associations.
- Integrated new datasets from ReMap.
New default database
- The TF-gene database bundled with TFEA.ChIP was built using the ReMap 2022 ChIP-seq collection and regulatory links from the ENCODE rE2G method. Due to memory constraints, the internal database includes only a subset of the 8,000+ available ChIP-seq experiments. Specifically, we selected 926 experiments performed in the ENCODE Project’s Common Cell Types, prioritizing broadly representative and high-quality datasets.
To download the full database, as well as other ready-to-use databases generated for TFEA.ChIP, visit
- <https://github.com/yberda/ChIPDBData>
- <https://github.com/LauraPS1/TFEA.ChIP_downloads>