GoekeLab/xpore: xPore 2.0

xPore 2.0 is a major release that implements the following changes:

• xPore now has 3 main running modes that replace the scripts in earlier versions:
  • xpore dataprep
  • xpore diffmod
  • xpore postprocessing
• Checking the version is now supported by xpore -v
• Changes in the xpore dataprep command as follows:
  • the pyensembl package is no longer required and supported to map transcriptome to genome coordinates. Please use the --genome flag and provide the GTF file (--gtf_path_or_url) and transcriptome FASTA file (--transcript_fasta_paths_or_urls) if you would like to work with genomic coordinates.
    • The option --summary is no longer needed and was removed.
    • xpore dataprep will no longer produce 'N' in k-mers.
• The documentation was updated to include these changes. xPore is still compatible with dataprep files generated with xPore v1.0.