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CHAMPAGNE 0.3.0

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@github-actions github-actions released this 18 Jan 18:58

New features

  • Find motifs in the genome with Homer. (#142)
  • Run motif enrichment analysis with MEME. (#142)
  • Annotate peaks with chipseeker. (#142,#147,#157)
  • Add preseq complexity curve and fastq screen to multiqc report. (#147)
  • Support multiple replicates per sample and call consensus peaks on replicates. (#129)
  • Implement differential peak calling. (#158)
    • Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.
    • If any sample has only one replicate, run MAnorm, otherwise run diffbind.
  • Print the recommended citation in bibtex format with champagne --citation. (#153)
    • CHAMPAGNE is also now archived in Zenodo with DOI 10.5281/zenodo.10516078.
  • The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)

Bug fixes

  • Fix deepTools plots (#144):
    • Per sample fingerprint plots instead of per replicate.
    • Input normalized profile plots.
    • Protein-coding-only versions of plots.
    • Ensure sample IDs are sorted. (#150)
  • Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)
  • Fix CLI profile on machines other than biowulf & FRCE. (#168)
  • Fix broken bold styling in documentation website. (#53)