Function reference • syntenet

All functions

angiosperm_phylogeny: Microsynteny-based angiosperm phylogeny.

annotation: Filtered genome annotation for Ostreococcus sp. species

binarize_and_transpose(): Binarize and transpose the phylogenomic profile matrix

blast_list: List of data frames containing BLAST-like tabular output

check_input(): Check if input objects are ready for further analyses

cluster_network(): Cluster the synteny network using the Infomap algorithm

clusters: Synteny network clusters of BUSCO genes for 25 eudicot species

collapse_protein_ids(): Collapse protein IDs into gene IDs in sequence names of AAStringSet objects

create_species_id_table(): Create a data frame of species IDs (3-5-character abbreviations)

diamond_is_installed(): Check if DIAMOND is installed

edges: Synteny network of Ostreococcus genomes represented as an edge list

export_sequences(): Export processed sequences as FASTA files

fasta2AAStringSetlist(): Read FASTA files in a directory as a list of AAStringSet objects

find_GS_clusters(): Find group-specific clusters based on user-defined species classification

gff2GRangesList(): Read GFF/GTF files in a directory as a GRangesList object

infer_microsynteny_phylogeny(): Infer microsynteny-based phylogeny with IQTREE

infer_syntenet(): Infer synteny network

interspecies_synteny(): Detect interspecies synteny

intraspecies_synteny(): Detect intraspecies synteny

iqtree_is_installed(): Check if IQTREE is installed

iqtree_version(): Get IQ-TREE version

last_is_installed(): Check if last is installed

network: Synteny network of BUSCO genes for 25 eudicot species

parse_collinearity(): Parse .collinearity files obtained with MCScan

phylogenomic_profile(): Perform phylogenomic profiling for synteny network clusters

plot_network(): Plot network

plot_profiles(): Plot a heatmap of phylogenomic profiles

process_input(): Process sequence data

profiles2phylip(): Save the transposed binary profiles matrix to a file in PHYLIP format

proteomes: Filtered proteomes of Ostreococcus sp. species

rcpp_mcscanx_file(): rcpp_mcscanx_file

read_diamond(): Read DIAMOND/BLAST tables as a list of data frames

run_diamond(): Wrapper to run DIAMOND from an R session

run_last(): Wrapper to run last from an R session

scerevisiae_annot: Genome annotation of the yeast species S. cerevisiae

scerevisiae_diamond: Intraspecies DIAMOND output for S. cerevisiae