Package index • gifter

All functions

as.data.frame(<gifter_dataset_traits>): Per-sample metrics joined to sample metadata
build_gifter_database(): Compile gifter source tables into SQLite
community_network(): Potential resource-handoff topology of a community
community_traits(): Quantitative traits of a genome-resolved community
database_changelog(): Read the curation history of the biological database
dataset_matrix(): One metric of a dataset as a samples by target matrix
dataset_network(): Potential resource-handoff topology of every sample in a dataset
dataset_traits(): Quantitative traits of one genome catalogue across many samples
evaluate_gift_cycles(): Report which derived cycles a genome closes
evaluate_gifts(): Evaluate genome-inferred functional traits
evaluate_gifts_community(): Evaluate a community of genomes from one annotation table
evaluate_reactions(): Evaluate reactions from observed genomic markers
genome_traits(): Quantitative traits of one genome
get_facets(): Get the curated facets of a GIFT or an anchor
get_gift(): Get a GIFT definition
get_gift_anchors(): Get the declared molecular anchors of a GIFT
get_gift_evidence(): Get the curation evidence recorded for a GIFT
get_gift_machinery(): Get the curated machinery of a non-metabolic GIFT
get_gift_pathways(): Get related external pathways for a GIFT
get_gift_reactions(): Get route reactions for a GIFT
get_gift_routes(): Get alternative routes for a GIFT
get_reaction(): Get a reaction used by gifter
get_reaction_systems(): Get enzyme systems, components, and accepted markers for a reaction
gift_cycles(): Derive the cyclic structure of the GIFT composition graph
gift_graph(): Derive the directed GIFT graph from shared anchors
gift_matrix(): The three-state call matrix, for export
gift_profile(): Derived ecological and physiological profile of each metabolic GIFT
gifter_community(): Bind genome results into a genome-resolved community
gifter_dataset(): One genome catalogue observed across many samples
gifter_db_connect(): Connect to a gifter SQLite database
gifter_db_disconnect(): Disconnect from a gifter database
gifter_db_version(): Report gifter package and database versions
gifts_by_facet(): Find GIFTs by a curated facet value
gifts_for_pathway(): Find GIFTs related to an external pathway
list_facets(): List the registered facet vocabulary
list_gifts(): List curated genome-inferred functional traits
list_reference_frames(): List curated reference-frame presets
map_markers(): Map observed genomic markers to curated components
reference_frame(): Define a reference frame of GIFTs
repertoire_distance(): Distance between genomes by encoded repertoire
sample_community(): One sample of a dataset, as an ordinary community
sample_id(): Sample identifiers of a dataset
trace_gift(): Trace the evidence chain for a GIFT call
trace_sample(): The GIFTs and genomes behind one sample's traits
validate_gifter_sources(): Validate human-readable gifter database sources
write_gifter_database_html(): Write an interactive HTML atlas of the gifter database