API

• orthomap - Command line functions
  • Command line function - orthomap
    • Command line function - cds2aa
    • Command line function - gtf2t2g
    • Command line function - ncbitax
    • Command line function - of2orthomap
    • Command line function - qlin
• Modules for dataset downloads
  • orthomap.datasets module
    • cazet22()
    • cazet22_orthomap()
    • ensembl105()
    • ensembl110_last()
    • ma21_fst()
    • mouse_ensembl105_gtf()
    • mouse_ensembl110_gtf()
    • mouse_synonyms()
    • mytai_example()
    • packer19()
    • packer19_small()
    • qiu22_frog()
    • qiu22_mouse()
    • qiu22_zebrafish()
    • sun21_orthomap()
    • ws288()
    • zebrafish_ensembl105_gtf()
    • zebrafish_ensembl105_orthomap()
    • zebrafish_ensembl110_gtf()
    • zebrafish_ensembl110_orthomap()
• Modules for eggnog
  • orthomap.eggnog2orthomap module
    • add_argparse_args()
    • define_parser()
    • get_eggnog_orthomap()
    • main()
• Modules for GTF handling
  • orthomap.gtf2t2g module
    • add_argparse_args()
    • define_parser()
    • main()
    • parse_gtf()
• Modules for NCBI taxonomy
  • orthomap.ncbitax module
    • add_argparse_args()
    • define_parser()
    • main()
    • update_ncbi()
• Modules for OrthoFinder
  • orthomap.of2orthomap module
    • add_argparse_args()
    • define_parser()
    • get_continuity_score()
    • get_counts_per_ps()
    • get_orthomap()
    • get_youngest_common_counts()
    • main()
• Modules for single-cell data
  • orthomap.orthomap2tei module
    • add_gene_age2adata_var()
    • geneset_overlap()
    • get_bins()
    • get_e50()
    • get_ematrix()
    • get_geneset_overlap()
    • get_pmatrix()
    • get_pstrata()
    • get_rematrix()
    • get_tei()
    • mergeby_from_counts()
    • mergeby_from_dataframe()
    • read_orthomap()
    • replace_by()
• Modules for query lineage
  • orthomap.qlin module
    • add_argparse_args()
    • define_parser()
    • get_lineage_topo()
    • get_oldest_common()
    • get_qlin()
    • get_youngest_common()
    • main()

Indices

• Index