rChEA3 0.2.0

Resubmission (CRAN)

This version addresses CRAN reviewer comments from the initial submission:

• Formatting Software Names: Added single quotes around software/API names (‘ChEA3’) in DESCRIPTION as per CRAN guidelines
• References: Added web reference to the ChEA3 API (https://maayanlab.cloud/chea3/) and original paper Keenan (2019) (doi:10.1093/nar/gkz446) in DESCRIPTION
• Writing Files: Removed default paths from exportResults() and saveViz() functions. The output_dir parameter is now required (users must explicitly specify their desired directory) to comply with CRAN policies

rChEA3 0.1.0

Initial CRAN Release

This is the first release of rChEA3, an R client for the ChEA3 transcription factor enrichment API.

Main Features

• API Interface
  • queryChEA3(): Query the ChEA3 API with gene lists to identify enriched transcription factors
  • Retrieves results from 8 collections: integrated rankings (Mean Rank, Top Rank), ChIP-seq data (ENCODE, ReMap, Literature), co-expression (ARCHS4, GTEx), and co-occurrence (Enrichr queries)
• Result Inspection
  • displayTopN(): Display top-ranked transcription factors across all collections
  • Results organized by evidence type with formatted output
• Visualization
  • visualizeRank(): Create publication-ready bar plots of TF enrichment
  • Automatic metric detection (FDR, p-value, or Score)
  • Customizable filtering and display options
• Export Functions
  • exportResults(): Export results to Excel workbooks with one sheet per collection
  • saveViz(): Save visualizations in PDF, PNG, or SVG format
  • Automatic date stamping for reproducible file names
• Example Data
  • a549_dex_downreg: Example gene set from A549 cells treated with dexamethasone (15 downregulated genes)

Documentation

• Comprehensive vignette demonstrating the full workflow
• Detailed function documentation
• README with quick start guide

Citation

Please cite the original ChEA3 publication when using this package:

Keenan et al. (2019). “ChEA3: transcription factor enrichment analysis by orthogonal omics integration.” Nucleic Acids Research, 47(W1), W212–W224. https://doi.org/10.1093/nar/gkz446