Package index
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MitoPilot() - Open The MitoPilot GUI
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add_samples() - Add samples to project database
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annotate() - Mitogenome Annotation Wrapper
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annotate_mitos2() - Annotate mitochondrial genomes using MITOS2
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annotate_trnaScan() - Use tRNAscan-SE to annotate tRNAs in a mitochondrial genome assembly
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backwards_compatibility() - Update old project database for backwards compatibility
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compare_aa() - Pairwise comparison of AA sequences
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coverage() - Map reads to assembly
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coverage_trim() - Use coverage info to trim linear assemblies
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curate_copepod_mito() - Annotation curation for copepod mitogenomes
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curate_diptera_mito() - Annotation curation for dipteran mitogenomes
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curate_fish_mito() - Annotation curation for fish mitogenomes
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curate_hexacoral_mito() - Annotation curation for hexacoral mitogenomes
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curate_lepidosaur_mito() - Annotation curation for lepidosaur mitogenomes
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curate_mammal_mito() - Annotation curation for mammal mitogenomes
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curate_octocoral_mito() - Annotation curation for octocoral mitogenomes
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curate_starfish_mito() - Annotation curation for starfish mitogenomes
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curate_turtle_mito() - Annotation curation for turtle mitogenomes
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custom_curation_db() - Generate a custom curation database
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export_db_to_csv() - Export project database to CSV
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export_files() - Generate export NCBI files
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get_assembly() - Get assembly from database
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get_assembly_userAsmb() - Get assembly from database
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get_top_hits_local() - Get top BLASTP hits
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make_PCG_alignments() - Generate HTML report woth PCG alignments
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new_db() - Initialize a new project database
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new_db_userAsmb() - Initialize a new project database
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new_project() - Initialize new MitoPilot Project
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new_project_userAsmb() - Initialize new MitoPilot Project with user-provided mitogenome assemblies
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new_test_project() - Initialize a test project
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nextflow_cmd() - Generate Nextflow command to run pipline
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params_copepod_mito() - Default curation and validation parameters for copepod Mitochondria
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params_diptera_mito() - Default curation and validation parameters for dipteran Mitochondria
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params_fish_mito() - Default curation and validation parameters for Fish Mitochondria
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params_hexacoral_mito() - Default curation and validation parameters for hexacorals Mitochondria
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params_lepidosaur_mito() - Default curation and validation parameters for lepidosaur Mitochondria
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params_mammal_mito() - Default curation and validation parameters for mammal Mitochondria
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params_octocoral_mito() - Default curation and validation parameters for octocorals Mitochondria
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params_starfish_mito() - Default curation and validation parameters for Starfish Mitochondria
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params_turtle_mito() - Default curation and validation parameters for turtle Mitochondria
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rotate_asmb() - Rotate circular mitogenome to start at given gene
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run_app() - Run the Shiny Application
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tbl_to_gff3() - Convert a GenBank 5-column feature table to GFF3 format.
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update_sample_metadata() - Update project database metadata.
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update_sample_seqdata() - Update sequence files for existing project
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validate_copepod_mito() - Title
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validate_diptera_mito() - Title
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validate_fish_mito() - Title
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validate_hexacoral_mito() - Title
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validate_lepidosaur_mito() - Title
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validate_mammal_mito() - Title
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validate_octocoral_mito() - Title
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validate_starfish_mito() - Title
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validate_turtle_mito() - Title