Function reference • metablastr

All functions
`blast2bed()`	Export BLAST output table to BED file
`blast_best_hit()`	Retrieve only the best BLAST hit for each query
`blast_best_reciprocal_hit()`	Retrieve only the best reciprocal BLAST hit for each query
`blast_genomes()`	Perfrom BLAST Searches Against a Set of Genomes
`blast_nucleotide_to_genomes()`	Perfrom BLAST Searches Against a Set of Genomes
`blast_nucleotide_to_nucleotide()`	Perform Nucleotide to Nucleotide BLAST Searches (BLASTN)
`blast_nucleotide_to_protein()`	Perform Nucleotide to Protein BLAST Searches (BLASTX)
`blast_protein_to_nr_database()`	Perform Protein to Protein BLAST Searches Against the NCBI NR Database
`blast_protein_to_nucleotide()`	Perform Protein to Nucleotide BLAST Searches (TBLASTN)
`blast_protein_to_protein()`	Perform Protein to Protein BLAST Searches (BLASTP)
`blast_protein_to_proteomes()`	Perfrom BLAST Searches Against a Set of Proteomes
`blast_repbase()`	Query the RepBase to annotate putative LTRs
`blast_rpsblast()`	Perform Reverse PSI-BLAST searches (rpsblast)
`detect_homologs_cds_to_cds()`	Perform CDS to CDS BLAST Searches against a set of CDS files
`detect_homologs_proteome_to_proteome()`	Perform Proteome to Proteome BLAST Searches against a set of Proteomes
`extract_hit_seqs_from_genomes()`	Extract sequences of BLAST hits in respective genomes and store it as `fasta` file(s)
`extract_promotor_seqs_from_genome()`	Retrieve all upstream promotor sequences from a genome
`extract_random_seqs_from_genome()`	Extract random loci from a genome of interest
`extract_random_seqs_from_multiple_genomes()`	Extract random loci from a set of genomes
`extract_upstream_promotor_seqs()`	Retrieve all upstream promotor sequences from a genome
`file_contains_aa()`	Helper function to check whether input file contains amino acids as required
`file_contains_dna()`	Helper function to check whether input file contains dna as required
`filter_best_hits()`	Retrieve the best hits across species from a BLAST table
`filter_homologs_core_set()`	Retrieve a core set of best hits that is shared across species
`filter_homologs_core_set_n_species()`	Retrieve a core set of best hits that is shared across at least N species
`gg_blast_hits()`	Plot `blast_nucleotide_to_genomes` Result
`gg_blast_hits_summary()`	Plot `blast_nucleotide_to_genomes` Result
`gg_hits_boxplot()`	Boxplot of a `blast_tbl` generated with `detect_homologs_genome_to_genome` or `detect_homologs_proteome_to_proteome`
`gg_homologs_one_to_one()`	Plot number of BLAST hits per species as barplot from a `tibble` generated with `detect_homologs_genome_to_genome` or `detect_homologs_proteome_to_proteome`
`gg_pairwise_orthologs_line()`	Plot number of pairwise orthologs for multiple species comparisons
`gg_species_dnds_blast_tbl()`	Plot pairwise dN, dS, or dN/dS distributions of orthologous genes
`gg_species_feature_blast_tbl()`	Plot pairwise feature distributions of orthologous genes
`gg_species_promotor_dist_blast_tbl()`	Plot pairwise promotor sequence distance distributions of orthologous genes
`list_outformats()`	List available BLAST output formats
`motif_compare()`	Count the number of motifs in a set of non-random versus random sequences
`motif_compare_multi()`	Count the number of motifs in a set of non-random versus randomly sampled genomic sequences for multiple species
`motif_compare_multi_promotor_seqs()`	Count the number of motifs in a set of non-random versus randomly drawn gene promotor sequences for multiple species
`motif_count()`	Count the number of motifs in a set of sequences
`motif_count_matrix()`	Count the number of motifs in a set of sequences and generate a motif count matrix
`motif_enrichment()`	Test motif enrichment in a set of non-random versus random sequences
`motif_enrichment_multi()`	Statistical assessment of motif enrichments in a set of non-random versus randomly sampled genomic sequences for multiple species
`motif_enrichment_multi_promotor_seqs()`	Statistical assessment of motif enrichments in a set of non-random versus randomly sampled gene promotor sequences for multiple species
`read_blast()`	Import BLAST output file
`read_blast_databases()`	Import BLAST output file
`sample_chromosome_intervals()`	Helper function to sample random intervals of length `interval_width` from chromosomes

Reference

All functions