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Changelog

Source: NEWS.md

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