ThorAxe’s documentation!

Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs

Check out our YouTube tutorial to see how you can easily use ThorAxe and visualise the results! If you want to know more, you can read our Genome Research publication.

If you find ThorAxe useful on your research, please cite us!

Zea DJ, Laskina S, Baudin A, Richard H, Laine E. Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Research. 2021 Jun 15:gr-274696. doi: 10.1101/gr.274696.120.

Note

ThorAxe can be run on the Ases web server, allowing for a convenient display of its output. Ases makes it easy to run ThorAxe and explore and share its results with others.

• Installation
  • Dependencies
    • ProGraphMSA
  • ThorAxe
  • Installation from source
  • Docker image
• Quick Introduction
  • I. Download transcript information from Ensembl
  • [OPTIONAL] Add transcripts to the previously download data
  • II. Run ThorAxe
• Command line programs
  • thoraxe
    • Named Arguments
  • transcript_query
    • Positional Arguments
    • Named Arguments
  • add_transcripts
    • Positional Arguments
    • Named Arguments
    • Input preparation
• Output description
  • transcript_query
  • thoraxe
    • Tables
      • S-exon table
      • Path table
      • Table of Alternative Splicing Events
    • Splice graph
    • phylosofs
    • Intermediate outputs
• Module API
  • thoraxe package
    • Subpackages
      • thoraxe.add_transcripts package
      • thoraxe.subexons package
      • thoraxe.transcript_info package
      • thoraxe.transcript_query package
      • thoraxe.utils package
    • Submodules
    • thoraxe.thoraxe module
      • add_s_exon_phases_and_coordinates()
      • create_chimeric_msa()
      • get_s_exon_msas()
      • get_s_exons()
      • get_subexons()
      • get_transcripts()
      • main()
      • merge_clusters()
      • parse_command_line()
      • update_subexon_table()
    • thoraxe.version module
    • Module contents

Indices and tables

• Index

• Module Index

• Search Page