Cerberus: triplet-based transcriptome aggregation and annotation

Cerberus is a set of command-line and Python tools to create triplet-based transcriptomes from a variety of input sources, compute gene triplets for different sets of isoforms, and produce triangular gene-isoform simplex plots.

Note: Cerberus is under active development and the documentation currently has some missing details. Please feel free to reach out through GitHub issues if you have any questions.

• Tutorials
• Transcriptome reference generation
  • Extracting triplet features from GTFs
  • Aggregating TSSs and TESs across multiple sources
  • Aggregating ICs across multiple sources
  • Generating a cerberus reference in h5 format
• Transcriptome annnotation
  • Assigning transcript triplets to a transcriptome
  • Update counts matrix with Cerberus IDs
  • Update GTF with Cerberus IDs
• Calculating gene triplets
  • Calculating gene triplets from Cerberus sources
  • Calculating gene triplets from a list of transcriptomes
  • Calculating gene triplets based on transcripts expressed in a sample
  • Calculating gene triplets directly from a GTF
    • cerberus gtf_to_triplets
  • Calculating gene triplets from custom subset files
• CLI API
  • cerberus agg_ends
  • cerberus agg_ics
  • cerberus annotate_transcriptome
  • cerberus gen_reference
  • cerberus gtf_to_bed
  • cerberus gtf_to_ics
  • cerberus replace_ab_ids
  • cerberus replace_gtf_ids
  • cerberus write_reference
  • cerberus gtf_to_triplets

Indices and tables

• Index

• Module Index

• Search Page