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