Changes in version 1.0.1 (2026-05-28)                  

New features

  - queryChEA3() gains a url argument so users can target a local or
    self-hosted ChEA3 instance instead of the public API. Defaults to
    the public endpoint https://maayanlab.cloud/chea3/api/enrich/.

                        Changes in version 0.2.1                        

Minor updates

  - Package now available on CRAN: install.packages("rChEA3")
  - Updated documentation in vignette and README: added installation
    instructions following CRAN acceptance

                 Changes in version 0.2.0 (2025-10-15)                  

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

                        Changes in version 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