Package index • MitoPilot

All functions

MitoPilot(): Open The MitoPilot GUI

add_samples(): Add samples to project database

annotate(): Mitogenome Annotation Wrapper

annotate_mitos2(): Annotate mitochondrial genomes using MITOS2

annotate_trnaScan(): Use tRNAscan-SE to annotate tRNAs in a mitochondrial genome assembly

backwards_compatibility(): Update old project database for backwards compatibility

compare_aa(): Pairwise comparison of AA sequences

coverage(): Map reads to assembly

coverage_trim(): Use coverage info to trim linear assemblies

curate_diptera_mito(): Annotation curation for dipteran mitogenomes

curate_fish_mito(): Annotation curation for fish mitogenomes

curate_mammal_mito(): Annotation curation for mammal mitogenomes

curate_starfish_mito(): Annotation curation for starfish mitogenomes

export_db_to_csv(): Export project database to CSV

export_files(): Generate export NCBI files

get_assembly(): Get assembly from database

get_assembly_userAsmb(): Get assembly from database

get_top_hits_local(): Get top BLASTP hits

make_PCG_alignments(): Generate HTML report woth PCG alignments

new_db(): Initialize a new project database

new_db_userAsmb(): Initialize a new project database

new_project(): Initialize new MitoPilot Project

new_project_userAsmb(): Initialize new MitoPilot Project with user-provided mitogenome assemblies

new_test_project(): Initialize a test project

nextflow_cmd(): Generate Nextflow command to run pipline

params_diptera_mito(): Default curation and validation parameters for dipteran Mitochondria

params_fish_mito(): Default curation and validation parameters for Fish Mitochondria

params_mammal_mito(): Default curation and validation parameters for mammal Mitochondria

params_starfish_mito(): Default curation and validation parameters for Starfish Mitochondria

rotate_asmb(): Rotate circular mitogenome to start at given gene

run_app(): Run the Shiny Application

update_sample_metadata(): Update project database metadata.

update_sample_seqdata(): Update sequence files for existing project

validate_diptera_mito(): Title

validate_fish_mito(): Title

validate_mammal_mito(): Title

validate_starfish_mito(): Title