CHAMPAGNE 0.3.0

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)
  • Optionally normalize p-values with the CCBR/consensus_peaks subworkflow.
• 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)