Release 1.1

• 2020-09-15: Prepare and try to release Sigflow 1.1. This is a version with its co-evolutionary R package Sigminer v1.0.17 and gold-standard de-novo signature extraction tool SigProfilerExtractor v1.0.17 as backends.
• 2020-09-14:
  • Add new command show to search cancer type specific reference signature indices and plot COSMIC signatures.
  • Support --refit in SigProfiler calling.
  • Fix a bug in identifying COSMIC v2 indices in signature fitting.
  • Upgrade sigminer version to v1.0.17.
• 2020-09-09:
  • Update README and documentation of input and usage.
• 2020-09-03:
  • Use sigminer v1.0.15 and support inputing reference signature index in fit and bt commands.
  • Allow users to decide if refit the signature exposures after de novo extraction with refit option.
  • Support matrix as input.
• 2020-08-14: Use sigminer v1.0.11 to use SigProfilerExtractor v1.0.15 to avoid issue raised from SigProfilerExtractor updates.